Hi Bruce,
That can happen due to the penalty for multiple translations. In other words, if you have a 100% match from one TM and only that TM is added to your project, then it will be counted as a 100% match, but if you have two different TMs, each with a different 100% match for the same segment, then each of those will be counted as a 99% match (assuming a 1% penalty for multiple translations) when both TMs are active in the project.