Please provide us with some errors, dialog boxes and so forth. See what shows up in the zimbra logs, maybe there are some authentication issues.
How are you attempting to pop3 the emails from the other two domains? You might have to use 'username@domain.com' as the login (not just username). Does everything function just fine with the webmail client?
I haven't done anything like this so take my advice as ramblings from a zimbra fan[atic]
Dallas