Certain files 'removed' from VCS tracking after "Save All"

Some files in my project get 'removed' from VCS tracking when I "Save All".

When I edit a file the color of the filename appropiately changes to the "changed" state. However when I use Ctrl+S to save some of the filename colors change back to their 'untouched' state.

When I run `git status` from the command line git tells me that the files where the color changes back after saving are not staged for commit.

I can add them manually with `git add .` and then they are staged for commit. However when I change those files they need to be added again using `git add .` again.

I'm using the default keymap so that's not where the problem lies.

Using PhpStorm 10.0.3 and git 2.7.1