IntelliJ save files disappearing from “Version control” view (GIT)

I'm using **Intellij Ultimate 15.0.2** with a java project and I got a weird bug with GIT.

I've set a save shortcut as I like the idea of saving files even if it's pretty useless in IJ (but anyway the bug is there even if using the "save in background" or "save while idle option").

Well, the issue is : Every time I hit the save button (or the auto-save is trigger) all my file in "9 - Version Control" -> "Local Changes" disappear.. I have to click on "Refresh" or "VCS->Refresh file status" to have it again! (in my git bash status everything's fine)

 - Here is my workspace before changing things :
 - After doing some changes and hitting save or having auto save :
 - The final workspace after clicking the refresh operation :

Does someone have an explanation or know how this would be fix ?

PS: To add to the weirdness of the issue, on one branch everything's fine, the issue is there only when I checkout this specific branch (which doesn't have anything special.)

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