Solved (kind of)
Well, I did figure out when this happens, and it's pretty weird. Still, this might be of help to someone.
If I have GPU-Z's executable on the root of a certain partition (in this case, D (non-OS, so no virtualstore malarkey)), it won't have CUDA ticked.
If I move it anywhere else, like D:\whatever\GPU-Z.0.4.8.exe, CUDA will be ticked. If I move it to the root of, say, the E partition, it works normally. So, in short, GPU-Z bugs out if -> D:\GPU-Z.0.4.8.exe
However, this doesn't happen on my friends' computers, who also have Windows 7 Ultimate x64 and Nvidia cards with the 260.99 drivers.
If anyone can come up with an explanation, I'd be very interested in hearing it :D