Git mysteriously deleting all files upon commit

I'm pretty new to Git (and version control in general) and am ashamed to say that this problem has been going on for a while now. Occasionally, after adding changes, git will delete everything from my repository upon the following commit.

Afterward I add and commit again, and it creates everything it just deleted.

It hasn't caused any issues, but I can't imagine this is a good thing, and I'm beginning to get more and more freaked out by it.

O开发者_如何学Pythonops. I'm just using the commands:

git add .
git commit -m "blah blah"