Mail.app not accepting incoming mail in .Mac Account

This problem has been getting worse over the last two months. Mail.app has been selectively accepting incoming traffic to my .Mac address, even those that I whitelisted through Rules and junkmatcher.
Incoming Mail from trusted sources, such as family and friends are not appearing. Until recently, subscriptions such as Versiontracker, Sundance, Apple Event, etc would populate targeted mailboxes, but now even they have not being accepted either.
This is very curious - because, if I access my .Mac accoun via WebDAV or another email client, the missing mail appears. After I manually accept an incoming message via a browser or another client and subsequently use Mail.app to view messages, the missing missives appear. I have not changed anything in either "Rules" or Junkmatcher. What has changed is system upgrades over time from 10.4.2 to 10.4.6. Now mail.app appears broken.
Any insights or fixes out there?
I will bring this up with the "Geniuses" at the SF Apple store. But for now, I'll be using another client until Apple fixes this.
G4 Dual 1.42 ghz MDD FW 800   Mac OS X (10.4.6)  

Every time I've seen something like this being reported, the problem ended up being a rule that wasn't working as expected, e.g. because a rule had specified any instead of all, or because a rule was routing messages to Inbox, or something like that...

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