Freeze up after boot

So, I have an interesting problem with my Computer. Running Windows XP SP3, Core2Quad, 4 GB RAM, I have two associated Raid Arrays (Mirrored on both). The OS runs on a separate HD. I boot the system, and it boots to the windows login screen. I can log in fine, and it starts to load windows, after about 10 seconds, it locks up. Everything, mouse pointer, everything...complete freeze-up. I tried to pull the raid arrays out of the mix, with no changes in the problem. I rebooted into Safe mode, opened up the MSCONFIG utility, and unchecked all the startup items. I rebooted, and jumped in and it seemed to load fine. So I went through each of the programs, one at a time, attempting to find the offending startup program. It came down to a loadup function called AhCSShell.exe which is a function of Autonomic Controls, which communicates from an external control source to iTunes. I shut that off, and it seemed to boot fine, but after running, it seemed to only delay the issue. Now, I boot it up and it'll take 3-5 minutes before it does the same thing. I set the MSCONFIG to startup in Diagnostic startup, and it still does it. Safe mode runs fine for any amount of time. Just to be sure I ran MemTest86+ overnight, and had 30 error-free tests. I'm fairly certain that it's a software problem, as opposed to hardware but I'm not sure what to do next.
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More about freeze boot
  1. Think of it logically. You have programs that start... everything is running fine, then 2 fat guys try going through the same door. What I mean is: mostly this kind of thing happens when 2 programs try to use the same interrupt. Freezing does have to do with hardware problems, but mostly boils down to either a network card problem or an conflicting interrupt problem.
  2. It's been running fine for several months. It just locked up and then poof, won't reboot. I'm actually running a seatools diagnostic on my OS HD right now, and it's detecting errors, so I may have to recant my former statement of "Not a Hardware Problem"
  3. I received 2 errors almost immediately on the Seatools long test, and received no more after that. I repaired the damaged sectors, and it seemed to fix the freeze up problem, but now windows runs pretty slow. Any ideas?
  4. I just installed a new HD, and put Win7 on it. Seems to work okay so far. I guess it was a HD.
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