Oh right, yea AE needs a lot of those default plugins to function. You could try removing any 3rd party plugin folders, but it's starting to sound more like an install issue. Still never experienced one like that though...
Problem solved.
It was a permissions issue.
I run After Effects as admin (something I started doing recently because of another issue with a plug-in).
I hadn't tried to run AME with AE open since I made the change.
When I changed permissions about two months ago I immediately had problems
with Bridge (which I use all the time with AE) that I fixed by setting it to also run as admin.
This suddenly occurred to me today as I was opening AME so I shut it down, opened AE and then ran AME as admin and it worked.
The final interesting thing is that this requirement that apps be running with the same permissions in order for some integration to function only applies when the apps are the same version. Using earlier version of AME (or bridge) worked fine with the current version of AE even when running with different permissions. 