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I have a really strange issue going on here on macOS Sierra 10.12.5.
After many, many failed attempts to upgrade SourceTree 2.5.1 to 2.5.3 when prompted by the automated update process (downloads successfully and appears to update successfully but version remains at 2.5.1 when the app restarts), I decided to download the 2.5.3c version from the website and install the new version that way. I have tried both overwriting the 2.5.1 version and deleting 2.5.1 before moving 2.5.3 into my Applications directory. SourceTree appears to remain at 2.5.3 until I restart my Mac, but when I launch SourceTree, I'm back at 2.5.1.
Any idea what might be going on?