Have just updated to 10.6.7 yesterday (29th March 2011) and am having the same problem re receiving emails to POP accounts. Tried the Apple solution at
http://support.apple.com/kb/TS3103, but of course, that was a complete waste of half an hour.
Tried the re-entering password/username trick, and that made no difference, either.
Like others, I hear the 'ping' and see emails are incoming, so tried the Spotlight search. It appears ALL my mail from 3 different accounts is helpfully being put into the Spam folder. Have tried playing with all the Junk Mail filtering options, but still no joy.
Mail has decided to disable the now incompatible Intego Anti-Spam plug-in I was using as part of my anti-virus/firewall protection, so I guess that might have something to do with it.
Thanks, Apple. Your so-called 'genius' has wasted half my business day, and meant I've failed to respond to several important business emails because I didn't know they were there.
UTTER FAIL.
EDIT: Have just uninstalled the complete Intego suite - seems to have done the trick. Mail now appearing in correct inboxes.