SourceTree doesn't show Uncommitted changes

I just upgraded to 2.0.20.1 (Win10) and things seemed to go smoothly... until I made all my commits (not pushed to remote yet) on feature branches. Then it showed Uncommitted changes at the very top of the tree, but it shows no files in the file status/log/history...except All files... If I check All files... then it lists every single file in the local repo!

But, in terminal, on my master branch, I do a git status, it says "nothing to commit, working directory clean..." I tried a reset hard to the last master branch commit and nothing changed.  

What is going on here? Will I be able to merge feature branches into master if some "part" of sourcetree thinks every file in the repo has been "modified" when they haven't been? (or have they?) 

How do I get it to be "clean" everywhere including the GUI view? Thanks for any help.