Fresh Install Blank Screen (sort of)

Hey all, after searching on microsoft's website, google and finally Tomshardware... I couldnt find anything close to what im experiencing.

My computer was working fine, no issues or problems. I decided to do a fresh install because it had been about 1.5 years. Thats where all the trouble started....

I have a legal Copy of windows and a Legal CD I bought from a store so piracy isnt an issue.

1) I tried to install windows 7 home prem 64 bit and i kept getting a Missing Boot Mgr message. I figured out that when windows was installing it wasnt creating the 100mb partition for system files and what not.

2) After fix that, my computer would not boot to desktop unless i had the Windows 7 CD in... I unplugged all other HDD's (2 Storage), Reformated and it worked.

3) Now once windows finished installing, I opened a few basic programs without installing any drivers or updates. Everything worked, left it up and idled for an hour no problems, ran tests on Mem and HDD no problems either.

4) I did my windows updates and it installed after which it prompted me to restart... I did and thats when the problem happens. I takes a very long time to boot into my desktop and once there, I have a 1920x1080 resolution (from 800x600) and i have no Icons, taskbar or anything but my wallpaper... if i press Alt + Ctrl + Del i get a black screen and if i press ESC i get my wallpaper background back....

5) I deleted the partition & reformated, and same issue after updates. The comptuer works perfectly fine in safemode and boots to my desktop... It is very weird. I ran Windows repair and I even open CMD Prompt and typed in the commands to fix the boot, fix the MBR and scan the OS, Everything was fix or operational... HELP!!!!

Any help would be grateful!!!

PC
Intel q9550, Gigabyte u3 motherboard, 6gb cosair ddrs XMS ram, EVGA 570hd GTX, thermoquiet 750watt powersupply, X-fi sound card (gamer edition), 22 inch LCD asus monitor, 3 HDDs - 500gb, 750gb and 160gb (750 & 160 are storage/important files), Corsair 500 Gaming Case!