I have the exact same problem.
I had a 9300 GS and was thinking that the video card was old an that was the problem but i recently bought a new 440 GT card from Gainward and it's the same! 100% processor 0% cuda. TMPGenc said at launch that it detects CUDA 3.1, did the necesary settings for it, but at encoding it shows very naturaly that cuda is used 0% ...
Does someone know why?
PS: I encode from AVCHD to BLURAY BMDV MPG.