Ok, I'm at my wits end here. I honestly don't know what to do. Here is the thing.
MB: ZOTAC NF780I-A-E LGA 775 NVIDIA nForce 780i SLI ATX Intel Motherboard
GPU: Evga GeForce 9800 GTX+ 512 MB
CPU: Intel QuadCore 9450 @ 2.66 (not overclocked)
RAM: 2x2GB Corsair XMS2 DDR2xtreme performance memory
HDD: 2xWestern Digital Caviar Black WD1001FALS 1TB 7200 RPM SATA 3.0Gb/s 3.5" in Raid 0
PSU: Rosewill RP600V2-S-SL 600W ATX12V v2.01 SLI Ready Power Supply
Optical Drive: I don't know some lightscribe DVD burner
The problem started to happen after I changed motherboard with new ZOTAC NF780i-A-E. Before that I had ASUS P5N-D LGA 775 NVIDIA nForce 750i SLI ATX Intel Motherboard and had 0 problems with it. But with new zotac motherboard my windows freezes on startup (after POST when the screen shows Loading Windows). Screen should show those bubbles that form windows logo but that doesn't happen.
The funny thing is that it happens every other time. I swear! It is so weird, I know exactly when it will freeze. Every other time I boot my PC like a clockwork.
Other thing I noticed is during the POST my PC all of a sudden (after changing asus motherboard) takes really long time to do a memory test. It will have a short freeze after it detects CPU. I will usually see "Memory Tes" - it will freeze there for a 10-15 seconds than it would display the rest of the testing word along with the memory diagnostic.
Note that none of these problem happened when I had asus MB but started whit my new Zotac MB.
Solutions I tried so far:
Reinstalling Windows 7. My first thought was that my installation got corrupted or something similar. I installed new copy of windows but the problem persisted. Than I installed windows again on different HDD (500 GB 7200.2 Samsung 16MB 3.5 GB/s) but the same thing. Please note that I installed same copy of Windows 7 on 4 different PC's in my home, none experienced any problems so far.
Updating BIOS. Twice.
Installing new MB drivers. Twice.
Installing new GPU drivers. Twice.
Changing RAM. I replaced 2x2 Corsair with another (new) 2x2 Corsair. Problem persisted.
Tried putting all 4x2 Corsairs in MB. Except memory testing that was 30-45 seconds during post, nothing changed.
Extensively monitored temps on GPU and MB for a week. Nothing unusual.
Other than problems I described my PC does not have any issues at all. It is very stable and I task it a lot. It is main storage area for my home network, it is turned on almost 24h, I have dual 32" monitor setup and I multi-task a lot. Never had a hiccup or temperature problem.
Well, if I had to guess to point at something you haven't tried yet, I would say that it is a RAM issue. Yes, you replaced the RAM, but have you tried messing with the timings? Try slightly slower settings.
One other thing, I have seen BIOS issues when the IDE/SATA drives are bad. Have you tried booting with no devices?