Fix CUDA being quiet and mark all CUDA_* as advanced

The if statement was wrong (didn't agree with comment) and caused
FindCUDA not to be quite on the first run. Also one of the
FindCUDA varaibles CUDA_TOOLKIT_ROOT_DIR wasn't marked as advanced.
While that one is the most important variable, similar variables
(e.g. ${FFTW}_LIBRARIES) is also advanced. It is only marked as
advanced if NOT GMX_GPU.

Fixes #1088

Change-Id: Id6d2c16e64688f1dd4bb3193017deb8b36c5c06e
Merge "Fix CUDA being quiet and mark all CUDA_* as advanced" into release-4-6