I'm listing this as a Vista problem but it seems more hardware related, though I've been unable to pin it down to any piece of hardware yet. I've looked around here and seen a lot of people with similar issues, but none matched my exact circumstances. Here's what I can tell you:
I built the PC a little over 5 years ago, and for the first 3+ years it was totally flawless. Somewhere around a year and a half ago I booted it up and it was several minutes to load to the desktop and then several more minutes before I could do anything, and even then it was incredibly sluggish. The HDD led would be on constantly, which first led me to believe that it was drive or controller related. The Vista resource monitor would show me HDD response times for processes of about 100x normal - up to 1500ms when I would see a max of 15ms-25ms in normal operation.
After several reboots things finally became normal. After that I found that I could reboot the PC and it would work fine, but if I powered it down for any period of time I experienced the same problem when trying to reboot. It seems that it has taken more tries to get it to work correctly as time has gone on. For a while I found that I could boot into the BIOS and leave it on the hardware monitor screen for 30 minutes and after that it would generally boot up fine. This has finally stopped working, and I can't always leave it on 24/7, so I had to look for a final solution. My gut told me it was the motherboard since there are so many things integrated into the motherboard, and it was likely that the conflict was there.
I recently had a family member's PC at home to do a clean out / reinstall, and it was mostly similar hardware, so I started swapping parts to try to narrow it down and prove it was the motherboard. I tried one component change daily, and immediately after each change it booted fine, but the next morning, I was at the same spot - dead slow boot. I swapped out the following parts over the span of a couple weeks: Memory, Video Card, Power Supply, Case, CPU... I can also eliminate the HDD because I swapped that about a year ago - after the problem started, and even with the fresh OS reinstall it persisted. With no problems found, I bought a used motherboard on Ebay - totally different brand and chipset. This didn't help, as it still failed to boot properly the following morning.
I have, thankfully found a work around to the booting problem, though it is not the solution. I have found that the reason I am able to boot immediately after a hardware change is that the power is totally drained. I found that if I pulled the aux 12v connecter (4 or 8 pin, depending on which motherboard I was using) to gain access, and then plugged it in again, things would boot fine after that. I've also found that if I turn the PSU switch on, then back off, then immediately press the case power button it drains the power and the PC will boot fine.
My question is: what is likely to cause this? It seems hardware related to me, but what are the odds that my original hardware and the piece I put in to test with are both faulty in the same fashion to cause the same result? The test pieces were all from a working PC, except the motherboard, which is the only unknown, though I am able to boot and use it after a change. Why does draining the power solve the problem? Note that I must flip the PSU on and off and then immediately press the case power button to make this work. I can tell if it will work, because if I have the case open I can see the CPU fan spin up until the power drains. If I am slow in the process the CPU fan won't spin at all. Also, if I do it fast enough, I can verify it by the motherboard's onboard LEDs - If I am too slow pressing the power button after powering the PSU off the LEDs will go out and the CPU fan won't power up to drain it.
Could there be anything OS / software related, like a WOL / WOR type of service that is giving some sort of feedback that is interfering with the boot?