The diagnostic of the drive came back clean, so it has to be the motherboard.
It would explain the bios settings randomly changing now and then (Before this main issue), and the slow startups i guess.
I doubt i would be able to play games and access the internet and access partition if the HDD was corrupt or bad, and there appear to be no bad sectors.
Both quick test and extended test got the green tick and "Passed"
Memtest will test the motherboard?
@Chemical, all my attempts to fix mbr etc were done in the Recovery console, booted from WinXP disc.
@baten PSU is in my spec, the TX 650Watt Corsair
I checked the volts they are fine, also if the PSU was so bad i doubt my PC would run games when i get a succesful boot. today i have had 2 succesful boots out of arround 20, and this second succesful boot i have been able to do the diagnostic. Anyway, my motherboard makes annoying beeping noises, and i recon when i reboot again im going to get another disk error. Shame i can't leave it on 24/7.
Another problem is my Anti Virus stopped working too after the crash caused by running the diagnostic the first time round. The diagnostic is the one from Western Digitals website, for my specific HDD.
So a quick conclusion:
Problems:
2 USB ports out of action on back of motherboard when in Windows - Seem to be fine on boot up to access bios
Bios settings sometimes alter themselves (Ie change boot priority)
Beeping noise from inside the machine instead of the default "Your doing something wrong" noise or w/e you want to call it, that is meant to come through external speakers.
Random succesful boots - allowing me to play games browse the net etc...
What i have tried/done:
Re-Install of WinXP
FIXMBR
Chkdsk
WD Diagnostic tools (Quick and Extended passed on the HD)
Swapping sata ports
Tinkering with bios settings
Checked voltages (Normal volts)
Checked temperatures (Normal temps)
Stocked my overclocked hardware
made sure everything is connected properly in the case (All connected/no loose wires/parts)
So it seems to be the motherboard.
Unless anyone else can indicate why it could possibly be the HDD.