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git diff no longer works in Update Project Info tab

OS X 10.8.3
IntelliJ 12.0.4


When I pull the latest from github, the Update Project Info tab shows the files that have been updated, but when I CMD+D to diff any one of them, the diff window shows the same file on both sides and it says "no differences" on the bottom, which is incorrect. Here's a concrete example:

application.properties is a file that contains our app's version number in a propety called app.version. I have this file open in the editor and it shows 0.8.139. That is the correct value, but when I diff this file from the Update Project Info tab, it shows 0.8.138 on BOTH sides.

I have several other projects which appear to be working correctly and I can't seem to figure out what happened with this one.

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