£100 ($170, €125) if you can solve my hardware problem (Longish)

If you have third party sata ports, plug one drive into the Intel chipset sata and the other into the third party controller. Might help
Not a perfect idea but worth a go that is for sure will add that to things to try.

Do you use any USB 3 devices?
Yes mainly Ext Hard Drives but nothing is plugged in while i'm trying to fault find this issue.

All1
 
'I can boot into both C & D drives as i wish'

mmm what boot manager are you using or just switching boot drive under bios ?
I instal using win 7 dvd onto C then from within C drive i just use windows explorer to start instal by double clicking the setup.exe so it's just the default windows boot manager.

so d is your std boot drive and not c, c is just plugged in in case d's OS go **** up?
why have c plugged in at all, just plug in if d dies.
Yes that's right D main drive and C will have the boot.ini on it and then i just bott into D, this is how i have had my system for years and always worked fine but this is becoming such a pain in the butt that i'm considering the USB/CD/DVD app route that someone has already mentioned at least it will get me up and running, i'm fed up using my old laptop.

All1
 
is having a full windows drive and setup for an emergency really necessary ? an ubuntu or similar usb stick would allow you to do the same
Agreed. This seems like a very complicated (not to mention time-consuming and expensive) way to accomplish something quite simple. Plus if you have anything genuinely important on the drive it should be backed up properly anyway.
 
If I wanted to run my setup with two separate Windows installations, I would:
- Plug in only one drive, install Windows from disc and all drivers/updates.
- Unplug that drive, plug in the other drive only, install Windows from disc and all drivers & updates.
- Plug in both drives, set your main drive as the default boot drive in BIOS
- If you ever need to boot from the backup drive, press F12 at POST (or the boot selection key if different) and select to boot from your backup drive.

Anyway, that's how I would do it. You only get the boot selection menu if you trigger it, otherwise the PC boots normally from your main installation without asking.
 
Install everything you need on drive C: including software, drivers, updates, etc. Then Download Macrium Reflect (free) clone your drive, and copy the image to drive D: and it should be 100% identical.

Then change priority in the BIOS under drive boot order.

That's how I would do it anyway.
 
Just create a windows PE disk then you will be able to go in and retrieve data from the main disk. Failing that use a backup software to make regular backups to an external disk or to the web.

I backup all my important docs and pictures to Google drive but also snapshot my drives every month using Macrium reflect.

Seems like a lot less hassle than the solution your trying to implement.
 
Try disabling this option, in power options - advanced power settings

http://i.imgur.com/xgyjt0u.png
Sorry Shivy011 that made no difference at my end still have same fault.

What happens if you install without using the executable, instead using pnputil -i to install the drivers from the inf files
That is an intresting point, i know nothin of this pnputil so will have to look intot hat but i did just going to device manager and selecting USB and made it look at my USB 3 folder where it does have an executable as well as inf files on there own and that has worked once.
I say worked i mean as in i'm able to boot into both C and D drives with no issues so that is perfect what i need to do now is test the USB 3 ports are running at USB 3 speed, so i'm going to try the above one more time just to be 100% sure then i need to find something to test the usb 3 drive.

I'll post back when i have some more info, some guys have said i'm going long way round and you may well be right, but this is how i'd like my system if i can, if not then i'll go along route of making one drive main boot in bios and if i need to switch to the other just change in the bios, thanks to everyone so far who has helped i think i'm getting there.

All1
 
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Couldn't you get clever here? Use RT-7 lite (IIRC) to build a windows 7 install that contains the all the drivers you want?

This could help skip all these exe verses pnputil issues? However, given the number of main boards that have this issue you may need to wait on MSI to release a fixed bios/firmware update?

Or simply use cloning software to copy teh drive C install onto drive D? That may be done at a level where it can't get so confused..
 
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I think this has been mentioned but can you not install Windows on your C drive, update everything, install additional drivers, AV's, firewalls, set everything exactly to your liking and then simply clone the entire drive?

I did exactly this using Acronis True Image then simply chose which drive to boot from in BIOS. I would always boot my faster Velocirator HDD but on the two occasions in 3 years this failed it was a simple exercise to switch the machine off/on, enter BIOS, select other drive and be back up and running in minutes.
 
Read cerefully, please = ammended.

Mate, I've got multiboot system as well - 3 Windowses and 5 linuxes, 2 bootmenus - everything on 3 drives (one SSD and HDD RAID-0 setup) and unfortunately Windows 7 bootmenu uses EBR and rest use MBR, so it's some kind of pain, especially once I disable one drive with no proper preparation each of them. Windows 7 is soo special ;-) and names boot partition with "C" always, so you probably know that - depending on boot, D drive points not always to the same physical drive, but other than boot one.

I think your problem is here. If I were you, I wouldn't plug in second drive until everything is installed properly @ both drives, but this must be done twice - separately, for each drive. Once it's done - I'd plug them both, boot* from C and use EasyBCD software to check if everything is fine with bootmenu* and drive assignments which I think are clue of your issue - not drivers**, not BIOS settings etc (and to re-create bootmenu files, if needed). After that, I'd boot* from D and use EasyBCD again to do the same thing. After that I'd be sure that disabling/taking out the second drive is fine for booting the whole machine, and not some "bootmanager file is missing" message. Blame me, if you still have USB issues with system built this way.

* boot, bootmenu - I mean Windows 7 bootmenu, so you must have 2 entires there. Booting via BIOS bootselector might cause issues as described.
** do not focus on drivers at all, mate. If it were drivers issue, you woudn't have working system booted from C drive. Please notice issues start with D drive = so it's all about drive assignments for 99%, as I wrote. Oh, and BTW, next time you might try this installing order: -Windows, 2-drivers (previously downloaded from website = newest), 3-Service Pack, 4-Updates.
 
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However, given the number of main boards that have this issue you may need to wait on MSI to release a fixed bios/firmware update?
Could you let me know what search string you iused as i have tried to goolge it myself but get nothing but reviews.

Or simply use cloning software to copy teh drive C install onto drive D? That may be done at a level where it can't get so confused..
If i can't find a fix in next day or so then this route or using some form of PE software is going to be my route and just settle for single boot drive, but i hate the idea of being beat.

You've replaced the entire PC and it still happens, seems like dodgy drivers to me. Are there any others?
To be honest i looked on Intel's site and only found drivers for there own boards but i also find intels site one of the most confusing going.
 
It seems strange that this would happen, as from a hardware standpoint - the two OS's are completely independent of themselves.

Excuse me if I skipped a little bit - but you said you can book into the OS, but can't use any USB devices. Have you tried using PS2/Mobile mouse applications to get yourself to log on and check the device manager to see what Windows is seeing?

May be worth after logging on in device manager if the above works to scan for hardware changes to see if it will reinstall the usb devices.

However from a data security and recovery point of view - its a bit of a rubbish system as its all manual recovery of files and applications - Would advise instead using a application like Acronis that takes snapshots, and then incremental backups so all your files are firstly safely in two locations - and also so you can quickly recover the whole OS state if the worst does happen.

At the moment you're essentially wasting 20 odd gig for something that a 50mb MiniXP boot CD could do. You have 16GB, if you want a secondary OS for when you're dicking about - it would be better invested running a virtual machine - it offers the same level of protection.
 
Some folks have mentioned my back up routine may be pants and image software etc, i never mentioned in in post as i didn't think it relevant but i do back up the folders i need to keep twice a day using an app called "ArkBackup" that then gets copied to 2 seperate 3.5 spinners (WD Black & WD Green) then i take at least one image every 24 by using "True Image", this image is then left on one single internal Black drive plus copied to another Black external drive and i upload to the cloud about once a month but that can be 10GB in size and given i'm only 800k (on a good day) upload this can take a fair while, the way this is looking is i'm going to be going with a single 256GB (Samsung 840 Pro) as my main OS and either another 256GB for my image back ups or maybe 512GB and look at some kind of boot disc that will allow me to copy files off or burn files to DVD, it's not perfect but i'm really getting fed up with whole situation
 
I haven't read the whole thread, so forgive me if this suggestion has been mentioned, or seems stupid :D

Have you tried installing windows 8 on the second hard drive ? You could download the free trial version. If it works with a dual boot system of Win 7 and Win 8 then you know that windows 7 is causing the problem.
 
Could you let me know what search string you iused as i have tried to goolge it myself but get nothing but reviews.

My bad I dont know why but I got it in my head you had an msi board rather than the 4 asus boards you've used sorry, I was referencing only this post

If i can't find a fix in next day or so then this route or using some form of PE software is going to be my route and just settle for single boot drive, but i hate the idea of being beat.

I didn't mean as a back up of your system to solve your problem. I meant get your install on drive c right, and then take an image of it, and install/restore the image to drive d? Alternatively couldn't you configure drive C and D as a mirror raid?

I still think making your own win7 install media could get you around this? Have you looked at RT 7 lite?
 
Have you tried changing the option "legacy usb support" in bios from Enabled to Auto? I find that this has solved a lot of un-responsive USB issues in my personal experiences. It sounds strange I know but worth a shot.
 
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