I'm seeing the same thing with my Yahoo account.
It seems like the BIS server can't handle filters from some POP/IMAP services.
When I have filters active on my yahoo account, I receive *some* of my mail, but when I login to Yahoo on my PC, there are a bunch of other mails that didn't get forwarded.
I've now disabled all my filters ... and I seem to be getting all mail now.
Including SPAM
