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This is a regression specific to macOS Mojave and the dark mode changes introduced. We've already got ticket(s) on this and will address in a future compatibility update.
Senior Mac Developer, Sourcetree
I can also confirm this bug. I was using Light Mode in version 3.2.1 then updated to 4.0. It was still in Light mode after restarting.
Curious to see the new dark theme (assumed it had changed) I switched to 'Use macOS setting'. Now I cannot change back to Light mode unless my macOS setting is light!
Its not possible to use Light Mode whilst macOS system is using dark