Man, I'm really banging my head on the wall on this one. Do you have other custom libraries or boards you've added (per your comment about "lots of libraries")? If so, where are
they located? I keep thinking this is some sort of version compatibility thing? As a side note, I'm a lab instructor a the U of Minnesota and there was a student I was helping get started with Arduino on his Win10 laptop. The windows, icons, and fonts were ridiculously small. I googled it and turned up plenty of hits.
Not that this is related at all... just precedent for Win10 being potentially "weird."
I googled around a bit for "board not showing in board manager windows 10" but didn't get anything obvious. There was
this github issue about the zero not showing up, but the resolution wasn't super clear. I
think the point had to do about the .json config for that board set not containing the zero at the time of the 1.6.5 release, but we're manually adding the url, so that doesn't make sense. I think the easiest would be to see if
any additional board can be installed and then figure out where it's living. Or maybe try a different installation of Arduino. I'm on 1.6.8 for reference.
Sorry I can't help more, but sounds really frustrating!