I did some more testing and found that my laptop needs a bit more patience, by increasing the timing parameters a bit I get consistent results:

-Dorg.eclipse.swtbot.playback.poll.delay=500 -Dorg.eclipse.swtbot.playback.delay=400

The last 2 tests consistently fail since EGit doesn't behave in the way these tests expect (verified that manually).

If you want I may upload my changes squashed to your patch.