"It" -being the head...doesn't have a compression ratio..but we know what you meant.lol
It's safe to assume one head had maybe .015 more milled from it than the other .
You should always cc a single replacement head. If they aren't a pair from the factory, and sometimes even if they are, they will be different. I've had one chamber by itself be 4cc smaller than the other 3 with a set of J heads. It shouldn't really run rough per say cause of that...but maybe the vj leaks or it's a drastic flow difference..some do more than others at machine shops. Some just touch the 45 and send it, others might do a deshroud.. who knows.