After installing my new motherboard, it's drivers, and reinstalling windows on a new hard drive I've been having problems booting. My computer is slow for anywhere from five to ten minutes after logging in, and by slow I mean I literally cant click on anything without my system locking up. After 5-10 minutes my computer starts running at full speed again. I've tried diagnostic startup (still boots slow) but for some reason it boots just fine, maybe a little slow in safe mode. During startup my CPU isn't overly taxed, and this happens even after disabling all of my startup programs.
Is there any way to troubleshoot this issue?
My system specs are as follows
Phenom II 965e
GTX 560 SLI (one of them added during the new mobo install)
Asus M4N98TD EVO (added right before reinstall that made the crashing begin)
Corsair Vengeance DDR3 1600mhz (added with mobo)
500GB HDD (Operating system on this before mobo reinstall)
WD5000 500GB HDD (OS on this after mobo install)
Cooler Master 700w PSU
See if it still happens if you start in safe mode. I know you've disabled all your startup programs, but if the issue doesn't occur in safe mode then there is undoubtedly some service starting with Windows that isn't playing nice.
I mentioned in the OP that it ran pretty fast in safe mode, although it wasn't perfect. The "laggy" period was about an eigth the time it was in normal boot. however this may just be the norm for windows.
Actually it boots only a tiny bit quicker in safe mode... I'm starting to think this is the hard drive's fault. One sec I can get the HDD benches. Plus my computer just BSODed about a minute ago for the first time since my broken sound card.
Also the WD5000 is my old HDD, my new one is a ST3500 or some ***.