I think the umpire must have taken the requirements to disengage the rubber and mistakenly applied them to taking the rubber. As described, the umpire was wrong.
And, while this *might* have contributed to a run scoring (the umpire didn't put the runner on third to begin with, and we don't know what would have happened if the umpire hadn't ruled a balk), the umpire didn't "cost" you the game.