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So I am on the master branch and choose to "Diff Against Current" on another branch but nothing happens. It does work on other branches and I am 100% sure these two branches which does not work are not identical.
I have committed and pushed changes in the same file to both branches and as I check out the other branch I can see with my eyes that they do differ. Therese a lot of obvious differences and doing a git diff will print me the changes. It's only in sourcetree where it doesn't work.
Hmm, do you have any text in the search box that's in the bar between the graph pane and the diff pane?
The most likely explanation is that the branches aren't different. (No offense: I don't know you or the situation with your branches, so I don't know how reliable your claim of 100% certainty is. Another recent question was 100% sure there weren't whitespace differences, then found whitespace differences.)
One way to confirm the branches aren't identical (and see a diff) is to merge them. The resulting merge commit will include all the changes from one branch to the other. I would recommend selecting the "force new commit (no fast-forward)" option in this particular situation, and make sure you do NOT push the merge so you have the option to safely reset your branch to the pre-merge commit.
If the merge results in a commit with changes, as you expect, take some screenshots and submit a bug report, because what you describe (if accurate) definitely sounds like a bug, not a user error or configuration problem. Bug reports go to jira.atlassian.com.