During the commit process, if you select "Stage File" in the diff viewer, this causes the "Working Copy Changes" view to reset it's selection to the top file. In the cases of cherry picking changes from a large change set, this is extremely annoying.

REPLICATION:

Use the attached script to create a git repository with a pending change set.

1. Execute the script in the Git Bash window to create a "commit-stage-problem" repository with a change set,
2. Open the repository with SourceTree,
3. Select "Commit",
4. Using "stage file" commit only the files which added cstdint
5. --> Every time you select "stage file" the working copy file selection resets to the top of the list again.