In the repository settings tab, it is possible to add extended integration settings, which can be used for e.g. pull-requests. Each time the application is restarted, the settings that were inserted dissapear and you need to be re-applied.

This problem is recurrent since some versions. I believe I have this since I use version 2 of SourceTree.

We use the 'Stash' version of the extended, and it is really helpful for Pull-requests, it's just a PITA that we need to re-apply the information each time we start-up the program.