Improved option disabling on switching to OpenMM build in a non-clean build tree

Improved option disabling on switching to OpenMM build in a non-clean build tree

When switching from CPU->GPU in a non-clean build tree it seems to work fine,
a few options are disabled/modified from the default values.
However, when doings GPU->CPU switch, the code builds, but the default values
(fftw3, threads, SSE) are not restores and need to be changed manually.