Mac Pro Late 2010 Windows 7 - no rear usb ports

I recently purchased a new Mac Pro 12 core and put 12GB of RAM in it. I have been having nothing but trouble with Windows 7 from day 1. I have used Boot Camp in the past and have successfully installed XP on my MacBook Pro, my quad core 1st gen Mac Pro, and the first gen intel Mac Mini. I have had no issues whatsoever.
I avoided Vista altogether because of the horror stories I kept hearing about but W7 was highly recommended to me by people who have it installed on their Macs. I have had zero productivity in Windows since the purchase of this new machine and it has been a huge regret. I have done 3 successive re-installs and keep coming up with the same problems. To give you some more info of what I have tried: Each time I install, I use the boot camp assistant app (in the Utilities folder) on the mac side, install my purchased copy of windows 7 64-bit, then once it's installed I put the Mac OS installer disc back in and let it install all the boot camp drivers (3.1). Finally, I go straight to the apple site and download boot camp 3.2. Everything seems cool except...
The 3 USB ports on the back of the machine as well as the top USB port on the front of the machine are completely disabled. Whether I have something plugged into the back or not, the ports do not work, however, I need to plug things in for the problem to show itself in the Device Manager in W7. (USB Root Hub (2 ports) - - Unused Port - - *UNKNOWN DEVICE*
Not only is this a total hit to not be able to use those ports, but this 'malfunctioning device' is causing the blue screen of death each time I try to shut down Windows. (the USB device... the hub itself?? nothing plugged into it)
I have also been trying to download a very large piece of software in Windows 7 and the main download is almost 2 hours. Since I've never actually sat down and watched the bar go by for that long, I never see when it happens... but I'll come walking back into the room and the computer is sitting there as a Mac!! What the ****?! Without warning!
I'm fried from this. Been eluding me since I got this computer. I'm about to just install the 32 bit XP... take the speed hit and be done with it! Unless somebody out there can help me with this problem.
Any additional information I can give you about what I've seen and what I've done is here. All of these problems exist only in Windows. The Mac side of this computer works perfectly in all areas.
I've seen the error message: Windows has stopped this device because it has reported problems(code 43)
Windows did not shut down properly (Get this error every time at startup)
I tried deleting registry files (really bad... had to completely repair W7... then did my 3rd re-install)
Does anybody have any idea of what is going on here?

Thanks Hatter. I have thought about a lot of this stuff in my trials and I'm still at a roadblock. A few things to note:
I agree that W7 Pro is needed for this machine. You had mentioned something about an electric ISO but I purchased the actual discs from Best Buy and have gone through the entire installation process a few times now. I forgot to mention in my original post that there is nothing 'cracked' in terms of software anywhere on this machine. Every single thing is legit and in most cases, coming from original discs.
I was hoping to avoid having to put Windows on a separate HD because then it would mean one less internal storage bay for my video storage drives (on the Mac side). Plus there's no guarantee that putting W7 on a separate drive will not produce the same results with the hardware (although I AM going to try this method... just to see if it clears up the hardware problem.) Rolling with this configuration long-term will be an absolute last resort thing but certainly not off the table. (I'll let you know if it works or not.)
For now, Windows 7 runs through boot camp on my new Mac pro. I have only 1 active usb port on the front (the lower one) which I use exclusively for keyboard and mouse... no choice. All other usb ports dead. All firewire ports seem to work fine. The machine also crashes on every shut down (sometimes with a blue screen... sometimes not) and reminds me about it on every successive startup. It also reminds me that windows has disabled a usb device on every startup. This hardware problem seems to periodically cause the machine to shut down and restart as a mac if left unattended for more than a few minutes. Basically, W7 is totally useless to me through boot camp on a boot camp created partition on my Mac boot drive. I will let you know I have success creating a separate hard drive as a Windows partition.
Any additional help is greatly appreciated! This one is really puzzling to me!

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