By watching files on disk change I can see if I go to Git->Settings->Source Control->Git Global Settings and change things like "Cryptographic network provider" I can see that it's writing .gitconfig in %HOMEDRIVE%%HOMEPATH% rather than %USERPROFILE% where it git seems to be finding my ssh configuration directory. Is there any way to alter this behavior? I'd like both ssh and git to look in %USERPROFILE%.
Also Git Global Settings seems to impose the email address of my msdn account over what is in the global .gitconfig file. Even if I change it in the settings dialog and hit ok, when I come back to the dialog it's gone back to the msdn address. So for that value, ignoring the .gitconfig file and not writing that value when edited.
There is also a bug here but I don't know if I should report this separately. If I go into Git->Options->Source Control->Git Repository Setting instead and change the email address in there, then the global user email value in the .gitconfig file gets overwritten to my msdn account address! I would expect changing the repository-specific address would not touch the global setting regardless of where they are stored. It does write into .git/config as you would expect. So the bug is writing to the global config file at the same time.