Could you please show a screenshot of the log illustrating the other branches that should be updated, too?

Which exact options should be respected?

According to my knowledge Windows behaves differently than Linux/MacOS. While Windows has a central place to configure environment variables, those on Linux/MacOS usually are configured in some shell scripts. But when launching a Linux/MacOS GUI application from its icon, those shell scripts are not executed and hence have a different environment. A quick workaround would be to start SmartGit from such a shell instead of starting it from the GUI icon.

This is no bug, but a change of Java: https://bugs.openjdk.org/browse/JDK-8187041

You can search a branch in the Ctrl+P popup.

Git only supports the concept of tracked *branches*, not tracked *tags*.

Why not commit/push even unfinished code into your feature branch? SmartGit offers all sorts of features to clean up this "mess" later, so it would look like done right from the beginning.

For backup purposes I'd rather recommend another remote.

Did you already check the preferences, page "Tools"?

You may help us by providing a sample file that covers all edge cases.