This .cfg works indeed, the problem seems to be about not starting life support and habitation on the SSPXR. The following picture shows two exact copies of a craft, the lower craft (in the ls-tab) is a craft that was launched long ago, with a fresh cycle of kerbals. Their hab timer matches the hab timer of the newly launched, identical craft that has not yet started its life support and habitation. The following image is of the hab timer after replacing the standard .cfg with your .c