I'm not having problems with the new version's stability, but I agree about the 'upgrade' email from Ritlabs.
I have sent them a query as to the upgrade price. I cannot understand why the 'normal' (i.e. not 50% off) upgrade price for existing (and registered) users seems to be the same as buying the product outright?! I have not received a response as yet.
If the worse comes to the worse, I'll back up my email, remove v.3, re-install v.1 and apply my authorisation key to it. I don't mind paying an upgrade fee if it seems good value for money. I am not going to pay the same fee as somebody who doesn't already own the product, though!
V3 is well worth it and those having problems with the default BayesIt spam filter should use Achim Winkler's very effective BayesFilter plugin instead.
I, too, have had numerous problems with BayesIt and gave up on it in the end.