I think the problem is that the old .threads used to store signatures in the posts and now with the upgrade signatures are displayed dynamicly. That is, a user's signature is added to the post during display and not during storage so it changes along with the poster's current settings.
I don't think it would be to hard a task to have it not display on posts older than a specific date/time. I'll try to look this over when I get a chance.
