This is preceisly why...
I got rid of the 2008 mac pro.. Make no bones about it... its a great machine, but it has SEVERE limitations and Apple is to blame for crippling its firmware..I will outline the flaws currently:
1. SATA ODD_Ports - usable on the Mac side(anything mac or mac os x, diskwarrior etc).. BUT NOT USABLE on windows - MAJOR reason for my switch.
2. VT-X - This was supposed to be fixed in Mac Pro(Early 2008) firmware 1.3 but failed to do that.. I phoned Apple a while ago and they duplicated the problem with the vt-x being disabled on the 2008. They promised a firmware update called 1.3.1 - NEVER CAME ABOUT.
3. IDE - While on the mac side you can use the odd_ports for hooking up two sata drives, you are still LIMITED to booting off them while under Mac OS X or Mac EFI boot screen, otherwise to make use of the odd ports under windows, you MUST install the AHCI drivers, but don't expect windows to finally boot from them once those are installed. While Windows recognized the odd ports finally, still booting from them is not fixed.
THE ONLY GREAT feature that the 2008 has and why it is surviving much longer than anticipated is EFI64 which you don't have on the mac pro EFI32 only system.. but you do have the ability to boot from the ODD ports into any OS you wish - Apple didn't mess up the firmware on 2006-2007 machines, but you are stuck FOREVER with EFI32 and only one graphics card from Apple will work: ATI Radeon 4870 HD.
The 2009 mac pro so far from what I have been told has no major limitations.. except it boots the windows installer in legacy mode.. AHCI is needed here.
I've changed my Mac Pro 2006 mostly because of EFI32 and it's bad smell :/