yes it is
the problem is a user friendliness problem
win xp or vista has drivers for ide/ata but not for the ahci sata mode on the mac pro motherboard
so to be able to easy install windows on bootcamp, the mac pro defaults to ide ata emulation when it boots to windows, this was the only way too make bootcamp easy for everyone, as searching and loading drivers during install is not exactly easy
only solution to this is to boot through grub to get to windows, grub can force the motherboard in ahci mode, but then you need to change your drivers in xp too, solution for my first gen macpro is in this thread:
http://forum.onmac.net/showthread.php?t=2739
i think it will work exactly the same on second gen but am not sure as i only own a first gen macpro
in os x the mac is always in ahci mode this only affect windows, also unless you want to use the extra ports on the motherboard of the macpro under windows this is not really an issue