Please visit the cudart downloads link to get the *hopefully* bug fixed versions of cudart for CUDA v1.1 and v2.0. The v2.0 one also includes the viewport bug fix.
Although the previous versions worked fine on the majority of systems there were issues with any CUDA 2.0 toolkit install / new forceware drivers. Hopefully these are now sorted out. Please make sure you extract all the files from the zips before you run the .exe's.
Thanks again to Audun for his help on this one. Its nice to see that there are still people out there who know how to use a debugger in native mode.