I have one repository that is always showing "Uncommitted changes" on the Log / History view, even though nothing shows in the list of pending files (see screenshot).  This is only true in the 2.0.x betas – in the 1.9.x release SourceTree does not indicate that there are any changes.  All the other repos I've opened in the beta display correctly.  This is my largest repo, and has a lot of ignored files, so possibly that has something to do with it?  If you need more info, or if there is something you want me to try, let me know.