Weird problem with new build..

I'm not sure this is the right place for this but I have an issue. I just upgraded to a new board, memory, videocard and cpu. I'm still using the same hdd and psu. I installed a fresh copy of windows 7 and everything booted up just fine with a decent post time. Now like a week and half after the install its taking forever to load. It will hang at the post check screen detecting the drives, then on the next screen it will hang, saying "loading operating system". It eventually gets passed this and will make it to the desktop but the system runs sluggishly. My first thought was that the PSU was bad because one of the output molex cables died on it and when I turn off the power switch for about a minute then turn the system back on, it will boot faster. So, I just installed a new Corsair TX750.. and the problem is still there. My next thought is the HDD but maybe it's the motherboard or the memory, I really don't know. Please if anyone knows the answer or can redirect me to the right forum that would be great. Also, I've scoured the web for an answer and this weird issue turns up a lot of results but no one seems to know why.. Hopefully someone here does  

Gigabyte 990FXA-UD3 (BIOS version 6.00)
Gskill Ripsaw DDR3 8GB
Phenom II x4 965
Radeon HD 6870
WD Cavier 160GB
Windows 7 x64