Reinstall Mavericks update
Ok, answer for the question was pretty much obvious -- you just go to the AppStore and hit 'Download' on Mavericks once again. It then asks  if you really want to reapply the once downloaded update. Just accept it and update will be reinstalled.

If you want to reuse once downloaded update file you could use advice from this question.

But the main problem (with jumping windows) wasn't resolved. To resolve it I used advice from this thread on apple.com. I've rebooted to safe mode and then rebooted once again to normal mode. After that the issue was gone. At least till now. Hope this helps to someone.