Unregistered VCS root detected

Hello, My project is configured to use Git. But every time I launch the application Git is not recognized and I get the same message. If I ignore it when I commit I get the message "No change detected".

So when I configure I get this window

first, my folder appear two times I don't know why exactly, but I select the unregistered one and click on + to add it, then it works.

I've just tried something, I realized for another project that I just have <Project> and it works fine, so I deleted the second "C:\probability", I can't delete the first. And now it works I still have the pop up telling me the root is not registered but if I ignore it I can commit. that is a strange behavior.