Since two days ago, my desktop has been having inexplicable issues, and despite tons of attempted debugging, I've been unable to track them down. I turn in confusion to you guys; hopefully you'll have some suggestions. First, specs:

2x 500GB HDDs, one primary/OS, one storage and backups
2x 2TB HDDs, mirrored (but not RAIDed) as storage and backups
2.4GHz Core 2 Quad CPU
Gigabyte motherboard
4x 2GB = 8GB RAM
650 Watt Antec PSU
2GB Radeon 6950 6-head GPU

Now, symptoms. A few days ago, my computer wouldn't come out of sleep, which it has done a few times before. On reboot, it claimed BIOS settings were lost and "recovered" them. Windows booted fine. The next time I rebooted, though, during the Windows boot process, right after the screen flash indicating (??) that my specific graphics drivers were loaded and activated, the pulsing of the Windows flag suddenly got much, much, much slower. It took another 5-10 minutes to get to the login screen, and although typing my password only lagged slightly, another 10 or 15 minutes to get to the desktop, and after hours the login process of starting up my programs wasn't complete. I was able to replicate the behavior several times. Troubleshooting items that I already tried:

>> Load Failsafe Defaults in BIOS. Same results.
>> Load Optimized Defaults in BIOS. Same results.
>> Tweaked BIOS settings to disable as much automatic CPU scaling and power management as possible. Same results.
>> Tried disconnecting all but the OS HDD. Same results.
>> Tried disconnecting all HDDs and booting a Windows install disk. Install environment displayed same symptoms, very very slow loading, very slow rendering of new windows. Did not actually start install process.
>> Tried moving OS HDD to different SATA controller on my mobo (it has 8 SATA ports). Same results.
>> Tried turning SATA to AHCI mode in BIOS. Windows repeatedly crashed and cycled on normal boot instead of getting super-slow. Turned it back to IDE mode.
>> Tried turning SATA to Native mode. Windows repeatedly said "Image loading failure. Reload image."
>> Tried booting an Ubuntu LiveCD. LiveCD booted at a normal fast rate. All operations seemed fast. Caveats: GParted refused to start. Switching to a terminal and running parted was inexplicably very slow.

Any thoughts would be very helpful. I'm hoping that "replace mobo/CPU/RAM" is not the solution, but it may have to be.

Side note: I smelled a burning smell that then dissipated last night - blown cap? Would that have anything to do with this?

Which version of Windows are you using?

Have you tried replacing only certain parts and seeing if the install disc works differently? If you have multiple computers, try a different motherboard, or different HDDs, RAM, etc. It might help you pin down the issue.

Windows 7. I should mention I did a memtest that came out clean, and the fact that other than disk access Ubuntu worked fine as a LiveCD should indicate my memory is at least no on its last legs. I don't have a spare functional motherboard, unfortunately. I have plenty of HDDs, but as stated, disconnecting ALL hard drives (although the DVD-RAM drive was still connecting) and booting a Windows install DVD displayed the same slowdown.

I'm not sure that the Windows install disc would be very happy booting into a machine that has no hard drives. My concern with Ubuntu is that GParted didn't work, which leads me to believe that the issue lies with your actual hard drive, or its relationship with your motherboard.

(For the record, I have no idea what's wrong, I'm posting generic suggestions)

Fair enough, I appreciate the logical thought. From the symptoms, I can only blunder about with a thought that one or more of the disk controllers on the motherboard is jamming up the bus or the Southbridge. That slow GParted was with a totally different, brand-new 250GB drive I had sitting on a shelf.

It might be worth checking that nothing is overheating, especially the CPU. A burning smell does not bode well.

I did, BIOS reports system and CPU temperatures at 30C and 33C respectively. I have a massive HSF combo on my processor, and my system has an array of 5 120mm fans that carry air front to back in my case. The burning smell was only there for a minute, and only after hours of testing things, but it definitely boded poorly for device failure.

Ah, I did have a problem with a Compaq once that had a heatsink and fan on the CPU but no extractor fan on the case. It filled itself with dust, clogging the heatsink and eventually cooking its own guts.

Have you inspected the inside of the PC to try to find the burnt component?

It is very weird that only Windows lags, and not ubuntu...
sounds like magic.

Were you able to mount your Windows partition and access its files from the Live CD?

- Souvik, I was indeed.
- aeTIos, I suspect, if it's a mobo/drive controller issue, that it has to do with Windows vs. Ubuntu drivers
- Benryves, I did not yet have a chance to do so; this is a brutal month at work for me.

Is your poor machine still slugging along?

I haven't had a chance to work with it the last few days. Last I checked, though, this situation was still the same despite a few more tweaked BIOS settings. This topic seems relevant, and I'm going to try 6GB instead of 8GB when I get a chance and see if it makes a difference:

http://forums.anandtech.com/archive/index.php/t-49904.html

hmm, this reminds of that one time my computer just became really slow. it was exactly as your computer was doing, taking forever to boot up, being extremely slow when it DID boot up. Heck, I booted into ubuntu from a flashdrive, and ubuntu was perfectly fine, no lag or eternal startups. I do believe that backing up my main files and restoring the computer to factory settings was what fixed it.

/me hopes this helps somehow.

EDIT: If I remember correctly this was happening because one of my files were corrupted. it said that it was 0kb and each time I tried deleting it, it would come back. that was probably the cause of the slow down....

Interesting, that's helpful to get confirmation of someone else having the problem without it being a hardware issue. I still suspect something in the BIOS, though, since even with all hard drives unplugged, the Windows 7 setup DVD takes forever to boot its stripped-down Windows environment.