The reason for storing the past hashes has to do with an attempt to avoid the kind of problem you're seeing -- an ever-growing number of post revisions being stored in the database under certain conditions. (For example, one case that came up a lot in practice was when users syndicated two aggregator feeds that sometimes carried the same items -- without a backlog of previously-syndicated hashes, you could get into a more or less endless "update war" between two sources, which would cause a new revision to be stored on every update). Now it sounds like in your cases something has caused the conflict-avoidance mechanism to break down, so that it is detecting far more "updates" than it should.
I'm currently making some changes and running some tests for the next public release of FWP, and if I could track down and make sure I've squashed the problem that y'all are running into, I'd be happy about that. So, could you (any of you, all of you) let me know:
(1) Which version of FWP you are using that gives you this problem;
(2) Which version of WordPress you're using it with;
(3) One or more of the URL(s) for the feed or feeds where you're seeing the problem;
and, if you know, (4) Whether the problem seems to be happening with every post on the feed(s), or only intermittently with some posts, but not with others. (And if intermittently, let me know an example of a post where you're seeing the problem.)