MSR has published lots of great papers but it has not yet replicated the success of PARC or Bell Labs by any means. I am not sure why this has happened, but it has been pretty obvious to everyone in the research community. Google, which came in with a research agenda pretty late, has more or less single handedly pushed the boundaries of industrial research in the last decade.
FWIW, as a researcher at a university, it is only my decision whether I apply for a patent or not. In contrast, patenting inventions is an inherent part of the research workflow at research labs such as MSR, Yahoo Research, etc.