Well, I figured out what is going on.
In updating a couple of footprints, some how I didn't get every single one of them of that name converted over to the newest version.
Which is odd, because I accidentally, used the tool to change every footprint on the board (not just the ones that I had just edited); and that was a mess because it moved almost every single silkscreen component on the board.
A couple of times it has happened that the "change footprint" dialog box did not give the expected results. At the time I figured it was just user error. However, thinking back. it does seem that some of this may be affected by the new library system with gibhub.
For example, when I am offline, I get this:
Errors were encountered loading footprints:
http GET command failed Cannot get/download Zip archive: 'https://codeload.github.com/KiCad/Labels.pretty/zip/master' for library path: 'https://github.com/KiCad/Labels.pretty'. Reason: 'IO_ERROR: curl_easy_perform()=6: Couldn't resolve host name from kicad_curl_easy.cpp : Perform() line:92'
It may well be that I have a library setting wrong.