It has come to my attention last night (Oct 1) that some users haven't been receiving emails from the system (pm notifications, new registrations, anything from the local server (pop3 email being uneffected).
After digging through the server and testing just about anything, I have the server sending data out as it's supposed to now. It seems the issue was that when messages where going out, the server assumed it was for local domains that it had MX entries for... Well, since we use Google Apps for our email (on every domain) the MX entry doesn't exist anymore (as of ~last week sometime).
The fix? Remove the domains from the CW config as they're not local domains, all mail delivered as it should be