I've set up Visual Studio 2013 with the native Git integration & BitBucket.
This has worked fine so far, but I noticed that Visual Studio stopped tracking newly created files (created through the IDE, such as simple new .cs files) for upload to BitBucket.
I experienced something similar recently but excluding and then re-including the missing files didn't work for me. In VS2013 Premium, I noticed there's a "Untracked Files" section at the bottom of the Changes window. It was simply a matter of right-clicking the files I wanted to include and adding them. Not ideal, indeed, but another work-around.