Windows 7 not booting after attaching HDD

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I have a Coolermaster case with an external HDD dock on the top (http://www.coolermaster.com/case/mid-tower/cm-690-ii-advanced-usb3/)

Today I put an HDD that had previously been installed internally without issue in to the dock (PC was switched off). When I switched the PC on I got a message 'Reboot and select proper boot device or insert boot media in selected boot media and press a key'

I reset the machine to no avail, then switched it off, removed the drive and there was no change. I've gone in to the BIOS to check the settings and I still can't get it to boot.

What else can I try to get things back to normal?
 
I seem to remember that the os puts files on other drives and looks for them on boot up. Have you tried installing the drive back where it was just to check and is the dock usb. If it is does it show in the bios?
 
Thanks, I gave that a go - no luck. It appears that connecting the HDD via the dock has somehow corrupted the boot process. I've tried using a USB recovery but my system is old and rather awkward at times. I can reinstall Windows, and might move to Windows 10 after this headache is sorted. Not ideal, but I'm getting frustrated with Win 7.
 
lifted from the web, but I've done this myself...

2. Partition not set as active.

This error will also appear if your primary partition is no longer set as 'active'. To set the primary partition as active, you need to use diskpart to run the necessary commands for this.

If you have the original Windows installation media, you can use that media:

a. Insert the Windows installation CD/DVD or USB and boot from that.
b. At System Recovery Options or the Troubleshoot, click Command Prompt.
c. Now type: "diskpart" (without the quotes) and press "Enter".
d. Next type: "select disk 0" (again without the quotes) and press "Enter".

NOTE: Where 0 is the disk’s number where your Windows is installed on. For a full list of disks that are available on your computer, type "list disk" (without the quotes).

e. Now you want to type: "list partition" (yes, without the quotes) and hit "Enter".
f. Here you will type in: "select partition 1" (you guessed it, without the quotes) and hit "Enter".

NOTE: Where 1 is your primary partition.

g. Finaly type: "active" (no quotes) and hit "Enter".
 
I'm not having a good day. I tried using the original DVD which gave the options of 'Install now' or 'Repair your computer'. I opted for the latter and got a message saying 'This version of System Recovery Options is not compatible with the version of Windows you are trying to repair. Try using a recovery disc that is compatible with this version of Windows'. I then tried the USB ISO that I originally used when I reinstalled Windows a couple of months ago - it wouldn't boot from that. I then burnt the same ISO to a DVD - this boots fine, but I get the same error message when I try to repair from it.

If I go to install a it as a new copy I can see that it sees the following:

Disk 0 Partition 1 - 128MB - MSR
Disk 0 Partition 2: Main Drive - 2794GB - Primary (this is my data drive, which has not moved)
Disk 1 Partition 1 - 465GB - Primary (this is my SSD that I normally boot from)

I've tried unplugging the data drive and switching the machine on, but it gives me the original message.
 
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