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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.
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.