Compare with same repository version not working (git)

phpstorm 2018.1.6

This only happens on one of two similar git repos.

If I make a change to a local file the Git / Compare with same repository version does nothing. I can see the diff if I show Version Control / Local changes and click refresh, then show diff on the file - but not directly from the editor pane for that file. git status also correctly reports.

This used to work until very recently, but I can't figure out what has changed.