IntelliJ resetting paths every restart

I'm seeing strange behavior in IntelliJ 2016.3 on OSX.  I'd been using PyCharm for a while, but recently needed to do some Scala development as well so switched to IntelliJ to edit both components in one program.  The problem I'm seeing is that if I edit the Module SDK in Project Structure to include additional modules in either a virtualenv or my default local Python interpreter, it works fine until I either checkout a different git branch or restart IntelliJ, at which point it forgets all the paths I added and I have to re-add them.  I've tried manually editing the jdk.tables.xml in ~/Library/Preferences/IdeaIC2016.3/options to see if that fixes it, but it still gets overwritten every time I check out a different branch or restart.  Has anyone else seen this behavior and figured out how to fix it?