Problem Outline
When booting from cold (and my machine is disconnected from main power when off, but leaving it connected doesn't help) the graphics card (single PCI-e card GeForce 460) will not initialise on the first boot, leaving me with the motherboards on-board graphics (which kick in automatically if no PCI-e card is found).
However, if I restart the computer - normally I do this by powering it off just after the numlock lights up on the keyboard (ie, just after POST/BIOS and before Windows takes over), wait for the system to whirr down, and power up again - the graphics card will work correctly. Once double-booted in this matter the system seems to work correctly - with no noticeable problems.
This is reproducible every time I try to boot - it has been working like this for about a month now.
Background Information
Sept 2010 - I suffered a hardware malfunction (crashes in Windows and graphics corruption on BIOS screens). By way of spare hardware I determined that replacing the PSU removed the issue, so I replaced the PSU with a brand new one of slightly higher power (460W replaced with 500W).
Oct 2010 - The problem resurfaced. I purchased a new graphics card (GeForce 460), which removed the problem. The new graphics card immediately started having the boot initialisation problems mentioned. I presumed there was a motherboard fault all along, but because the system worked once booted, and I was temporarily out of spare money, I left the system alone and continued to use it.
Early/Mid Dec 2010 - In the space of 5 days I recieved 3 instances of hard drive corruption (seemlingly fixed by chkdsk and sfc in each case...). Since I was already under the impression the motherboard was faulty, I purchased a new one ASAP, this also required new RAM (as I dropped from 4 slots to 2 and didn't want to drop mem quantity).
Past 3-4 weeks - With a brand new PSU, Graphics Card, Motherboard and RAM I'm suffering the problem outlined above.
So, what could be causing this and how do I can resolve it?
Additional Notes
Once double-booted the system seems to work entirely correctly.
The graphics card problem has occured on two entirely different motherboards.
I do not have the opportunity to test the graphics card in a different computer (I've only the old motherboard, which is dubious, or a really old desktop that still has an AGP port).
Under load (ie, modern games for long enough for temperatures to plateau) the system remains stable and performs as expected.
The software that came with the new motherboard and SpeenFan both report all voltages and temperatures are within nominal bounds, when idle and when under load.
I've looking over the BIOS settings for my motherboard multiple times and can find nothing that helps.
This system is configured to run with everything at standard levels - no overclocking.
I've tried booting the system with only the mobo and graphics card connected (thinking maybe my new PSU was too weak for the new gfx card, even though it meets the quoted PSU requirements for the card) but the same problem persists (and really if the PSU was weak I'd have problems with the system under load).
When the gfx card does not initialise the fan on its cooling unit is running, possibly slower than otherwise - but this measurement is by eye and so unreliable.
