I have over a dozen different email accounts, all with junk filtering enabled. At present, when I process my Uncertain folder (I've replaced all the individual Uncertain folders with a single search folder), I have to manually run the junk mail filter on each account, to iterate properly, make sure I haven't regressed, and minimize total trained messages. This slows me down somewhat, but I also wonder whether other people would simply leave this phase out — and since I don't know if TB necessarily ever goes back to automatically re-run the junk mail filter on old messages, it might be possible to get somewhat out of whack.
So I'd appreciate having an extra toolbar button available to re-run all junk mail filters. I don't know how hard this would be, but I'd certainly be available to help test (pre-)alphas, and perhaps even help in the coding.
The problem with "rerun all junk mail filters" is that that can take a very long time if you have lots of emails. I don't ever do this operation for my junk mail management, and I don't really see the need. But it is not difficult to add such a feature, so let me add this request to my bug list as a new feature request.