I built this system 1.5 years ago and it's run flawlessly until yesterday after I pulled the plug on my UPS (Belkin 750 VA) to clear the deck for the carpet cleaners. My computer was turned off, not in sleep or hibernation, but I had neglected to turn off the UPS before I unplugged it. Of course, it let me know by immediately sounding an alarm and I then shut it off. I realize that the computer would have been drawing a few watts but I figured the battery would have supplied that power for the few seconds between my pulling the plug and turning off the UPS. Also, I wasn't worried about a power surge, as the UPS provides plenty of protection.
 
After the carpet cleaners left I plugged the UPS back in, turned it on then powered up my computer, and I heard the usual one short beep. But it took about 5 min to check the CPU and Ram and write the results one character at a time then another 10 min to check the drives and complete the POST. Then Windows started up at the usual speed and everything worked fine...browser, email, word processor and spreadsheet. The only difference I noticed in Windows was that the icons on my desktop had been rearranged. When I turned my computer on this morning it did the same thing as yesterday...15 min to POST.
 
If anyone has any idea of what I might have done and what I need to do to correct it, please let me know. My level of knowledge is probably intermediate; I know how to build  basic system, load the operating system and drivers, and set the appropriate settings setup, but that's about it.
 
Here's my system specs:
 
Biostar TForce 550
Athlon 64 X2 4200+
Crucial XMS DDR2-800, 3 GB (2 x 1 GB + 2 x 500 MB)
Thermaltake TR2-500W
Gigabyte GForce 7300GT
Creative Audigy SE
Linksys Wireless G
Win XP Pro with all updates
iiyama E431S LCD Monitor
Belkin 750 VA UPS

1. You had your computer on and plugged into a ups which was plugged into your wall outlet.
2. You turned off your computer.
3. You pulled your ups cord out of the wall outlet while your computer was off, but plugged into it.
Is that the sequence?

This is very likely not caused by you unplugging it.  You may have knocked something loose while moving your computer.  Have a look inside and while you are there, blow away any dust and re-seat everything you think may have come lose.  My best bet would be a HD cable coming lose.  
 
Double checking?  Are you saying everything is normal after everything loads?

Yes. The computer was off but the UPS was on. I turned the UPS off within 10 seconds of unplugging it.

If you have a way to test your system (Hardware) and power supply, I would start there. I just read about a similar problem that said its possible you damaged your power supply and your PSU is causing the slow post.
 
Gotta run to Grandma's with the kiddo's. Good luck and Happy Easter to everyone.

Yes, everything seems to be fine after the POST and Windows starts up. I ran it for  few hours last night and its been running for four hours today. I've opened and used programs and they all work fine, and there's no noticeable loss of speed.
 
The cleaners worked around my desk, so the computer wasn't moved. I may have tugged a bit on the wires when I set the UPS on my desk, but everything seems to be connected properly now.

Try this.  I work as a computer tech, and a cheap trick we do at work is unplug from power, and press the power button a few times, maybe hold it.  Sometimes it helps discharge any static that may have built up in the circuits or anything like that.  I've seen it work before.  Can't hurt, just unplug your PSU from the UPS, leave everything else plugged in and try that, then plug back in and start it up.  

Well, I tried to shut it down to check connections and discharge static but it hung on "Saving your settings..." I waited for half an hour and saw lots of flickers from my drive light, so I left it for another 40 minutes to see what it would do. When I came back I found a message telling me it was unable to save data for file\DeviceHarddisk Volume 4\$Mft. So I shut it down with the power switch, unplugged it, checked all my power and drive connections, and tried discharging static with the power button as suggested.
 
When I rebooted it only hung on the memory test for about 30 seconds then completed the POST and Windows started up as usual. I suppose the fact that it was warm from running for five hours could be a factor in its starting so quickly, but not without some difficulty.
 
I used Device Manager to check the HDs and SATA controllers and ran a speed test on each drive (I have two SATA HDs running off the primary and secondary channel of the first controller) and found everything to be working properly and at the usual speed.
 
I can take the power supply out of my backup computer and put in this one to see what happens, but I'd rather not have to go through that until I've ruled everything else out, as it took me about an hour to get this octopus installed and connected. All the fans are running and there seems to be enough power to load programs from and save files to my HDs, so I don't see how it could be a PS problem, but I'm not an expert on this.
 

I just tried opening programs and files on each drive, and saving large files from one drive to the other (in both directions, i.e., from C to E and E to C) and everything worked fine, including the speed.

And I ran memory and processor tests, which were fine. I know they both pulled a lot of power and there was no indication that there was any lack of power for the tests. So I'm sure I'm getting lots of power, although I suppose there could still be something flaky about the PSU that's not making itself apparent.

Update:
My computer has been running for nine hours now, so it's definitely warmed up. I restarted it (hot booted) and it shut down and restarted perfectly. So I turned it off and turned it back on (cold boot)...also perfect. So I'll let it sit overnight and see if I have problems in the AM after its had all night to cool down. If I have problems in the AM I'll break down and swap power supplies unless anyone has other suggestions. Does anyone have any idea why it would start OK when its hot but not when its cold? This is a totally new development, not something that's been building up for a while.

I'm starting to wonder, you say you tested your memory.  Because you said it hung on the memory test for 30 seconds, and the guys were all cleaning around it.  Could be possible a stick of ram got shorted.  But with today's prices that's not a big deal.  Maybe try retesting one stick at a time to be safe.  

I've got plenty of RAM, so I can start removing and replacing it if I have problems in the morning. But I don't have much hope for that solution, as I ran two separate memory tests and they both indicated no problems. Also, the POST shows 3 GB, which is correct, and I don't get any error beeps. It's not the memory check itself that's slow, it actually appears that that may be happening quickly, but the results are written to the screen very slowly, one character or half character at a time, the same as the CPU check.

Part of my reason for testing the RAM was to make sure  was getting power. But I also know that faulty RAM can cause some strange problems.

What are you testing your ram with?  Try memtest.
 

 
No hdd??  Have your run your manufacturers hdd utility?

This morning it started up with no hesitation! So I'm going to take a wait and see approach. Hopefully you won't be hearing from me again on this problem.
 
Thanks to all of you for your help.

You may want to update your bios. Also you may have to reset your bios setting to get the system to boot the right way as well.
 
also some how boot from network may of been turned on.