Whenever I just delete any one file from the working directory, so that this is the only difference from the latest commit, the graph is wrong (version 3.1.3):
It shows me "uncommitted changes" not in relation to the latest commit, but to the one BEFORE.
The graph is correct, however, when there are just (or additionally) changes to files.
(gitk, for instance, still shows it correctly, so there seems to be nothing wrong with the database contents.)
Can anyone else confirm?
the attached screen shot should answer your questions.
For everything else: just pick any project you like in SourceTree 3.1.3, go to the HEAD, (clean WD) and then REMOVE ANY ONE file from WD. Worked for me for a number of projects, will likely work for you too -- and then you can see for yourself.
Thank you and kind regards!