Hey brett.r,
what kind of GPU do you have? macpro means discrete GPU. do you really have an ati2400 or ati2600 PCIe card? why don't you get a bit beafier one, like 4850 or something? it must not be genuine apple.
check out netkas' place (http://netkas.org), you can find lotsa useful information and custom roms for non-apple branded GPUs.
on the other hand, it still need to be a "supported" one, by supported i mean, even netkas can't turn water to wine, the drivers always come from apple. the custom roms just enable you to use an oem hd4850 (by gigabyte, sapphire or asus) or a bunch of other GPUs what are also sold by apple in your macpro. it costs a lot less than the "genuine" silver coloured apple ones.
back to your issue. apple tweaked the driver in 10.8 naming. i got confused too. you see in /S/L/E ATIwhatever.kext, there are a bunch of them. however because of info.plist inside them, some of them show up as AMDwhatever. for example the kexts needed for the 2400/2600 GPU freeze issue, are ATISupport, ATI2400Controller and ATIFrameBuffer, and since 10.8.2 they show up as AMDSupport/AMDFrameBuffer, and so on. ATIRadeonX2000 is however a cuckoo's egg. we need to use the most recent one, and the filename (ok, folder name) and how kextstat displays it, are the same.
go and check whether "kextstat | grep AMD" produces any output.
so i suggest to doublecheck what kind of GPU do you have in your macpro.
clean install will not help. (sacred druid rites, root magic, whatever)
usually no app touches your system drivers.
repairing permissions will only help, if you (un)intentionally changed the permissions: e.g. kext files are not owned by root:wheel, no extended attributes, dirs have 0755, files inside dirs have 0644 permission bytes.
in case they don't, OSX will not load those kexts, thinks they are not safe to load. nor will kextd use them to
build the kextcache. but it just doesn't go under the radar. you should be able to spot some messages in /var/log/system.log (like foo.kext failed to load, or something similar).
if you have the same issue that we have, and the 10.6.2 kexts does not help you, then you can still
get another GPU. you should be able to get some better one under $100 w/o any problems. like ATI4850 or 5770, or even better ones. just check what is available in apple's range (http://store.apple.com/us/browse/home/shop_mac/mac_accessories/displays#m.produc tKind=graphic_cards), and look for the same models at netkas, to find out whether there's a modded rom for them. then go and buy one in the nearest pc-shoppe. it will be a lot easier, compared to our mxm-whatever based GPUs.
plz report how it worked out, as i see, you are kinda first with a macpro around here, sharing the same fate.
