In case anyone else has the same problem: When connecting the editor to Git Source Control, it doesn’t seem like you can use the cygwin version of git. When I connected mine to a GitHub installation, it seems to work fine though.
So:
Path: E:\Programs\cygwin\bin\git.exe - Bad
Path: C:\Users\MyName\AppData\Local\GitHub\PortableGit_numbers\bin\git.exe - Good