Hmm... most of my exposure to Microsoft CS papers was in the late 1990s/early 2000s. Perhaps things have changed, or maybe it was just the set of authors that I read. In any case, the layout was markedly different, and once my friend pointed out that it wasn't just in my head, that they weren't using LaTeX, it was hard for me to un-see.
I used to collaborate with MSR and never saw anything but LaTeX being used. If you look at the level of sophistication in many of their papers it’s not something Word can even begin to achieve.