Cold boot problem - Motherboard or CPU suspected

[Robogoat]

Computer specs:

Gigabyte GA-P35-DS3 motherboard
Intel Q6600
512MB 8800GT
2 x 1GB Corsair 800Mhz DDR2 RAM
500GB WD HDD
Cooler Master Real Power 550W PSU

My story:
The problem I am experiencing with this computer occurred when, and only when, it has been turned off for at an hour or more. After I press the power button the computer seems to totally ignore me and will not turn on for a random amount of time. No fans start up, no LED's blink, no noise is made. Usually this would indicate a dead PSU or motherboard except when I accidentally left it turned on, about two hours later I returned to see it had started fine. That night I turned the computer off again and encountered the same problem! Basically, it's a 2 hour lag from hitting the power, and the computer turning on. I know the power supply is working because when a flash drive is plugged into a USB port, the LED inside will illuminate.

Now after I turned the computer off the other night it still hasn't started.

SUMMARY

When attempting a cold boot it takes anywhere between 30 minutes to 6 hours for the computer to start. During this time the only sign of life comes from my iPod being able charge when plugged into the USB port. Once the computer started everything ran fine, with the exception of the paused BIOS clock.

nVidia stress test and Micro-Scope diagnostics find no problems.



I have tried previously, and again since it's not turning on at all:

removing components and cleaning all terminals (nothing)

trying to cold boot with 1 stick of RAM (neither worked)

using another PSU (nothing)

using the current PSU in another computer (it worked perfectly)

booting outside of case to rule out shorts (nothing)

jumpering pins to rule out bad switch (nothing)

attempting cold boot with minimal components (nothing)

Is there anything else I can do to keep faultfinding? At risk of sounding stupid, I checked the CPU contact pins before and did not see any scratches or cracks etc and given it survived being worked at 100% usage for 2 hours and stayed below 60C with a stock cooler it's also prettymuch in the clear.

Let me know if you need more information. Thanks for your help!

[SecRecy]

See this thread for more suggestion : XP Crashes first login following cold boot...
http://forums.techarena.in/operating-systems/905940.htm
Blank desktop after login
Boot Partition Corrupted -- Repair How????

[unidentified]

How old is your motherboard. If it is under warranty then try to raplace it.

[CapriAnupam]

You can try changing the CMOS battery with a new one. The CMOS batteries come cheap. My cousin's PC had a same problem, turned out that the CMOS battery died. Worth a shot.
The "paused BIOS clock" gave me this thought.

[Robogoat]

Update: I was able to borrow a friends computer today and installed my RAM, graphics card and HDD and everything started fine. He didn't let me swap CPU's over though which was really the only thing I wanted to do haha.

SecRay, unfortunately those thready didn't really help me. I can't even get fans to start, let alone POST

CapriAnupam, I've tried that too (forgot to add it in) but that doesn't help.

Unidentified, your idea is starting to sound better and better now. I've been thinking of doing that for a while but just want to make sure I've done everything I can first.

Any more ideas? All help and suggestions are greatly appreciated!