I had successfully set up a Github repository in 3.3. After upgrading to 4.0 (and trying to enable submodules for that repository), Bamboo wouldn't load my repositories, complaining that the (still cached) username was invalid. The plan would still check out the repository and run just fine despite this, though.

I tried deleting the repository and re-creating it so I could make my changes, but I was still unable to get it to load anything.

I then tried to create a regular Git repository that happens to be on Github, which succeeded, although the "Duplicate username" message when a username is provided in the repository URL is rather confusing.