That isn't it. I know because if my capital ship wins the TM coin flip then I've seen it where mine gets really far out in front of the other capital ship when it's is the same opponent. The two turn thing has only happened a few times it's typically not that bad, but there are plenty of times where they get half or 3/4ths a TM bar ahead of mine.
My thought was what the first guy said and that each turn would be a coin flip. That doesn't happen though. If you guys do a similar mirror match check it out sometime. It is very irritating and obvious when you pay attention to it