Git change markers disappear when editing file

I've started having a weird problem over the last few days. I have a project in IDEA 13.1.4 under Git version control. When I edit a file, IDEA marks it as new in the editor tab (green filename) and doesn't show change markers for the edits I have made. Additionally, it doesn't show up in the Local Changes window until I click the Refresh button, after which IDEA marks the file as modified in the editor tab (blue filename) and the change markers appear. If I make some more changes to the file, it immediately changes back to being marked as a new file without change markers.

This wasn't happening until recently. And it only happens for this specific project (which is quite large). Other smaller projects don't exhibit the same behavior. I've tried invalidating caches and restarting but that hasn't helped. I don't want to have to reclone my repo because I have quite a few local branches, but I will if I have no other choice.

Any advice?