POP3it PRO SE not downloading email from certain servers

We migrated our FileMaker 10 server data to a new server running FileMaker Server 11. The server runs a script for one of the databases that uses POP3it Pro to check for new emails on a server and download them into our database. It worked fine under the FM 10 server, when we move the databases and setup the FM 11 server we've discovered an odd glitch. POP3 it Pro will download emails properly except for emails coming from one specific mailserver. This mailserver (Let's call it MainServer) happens to be a separate mailserver that we run. The mailserver for FM and MainSever are in different physical locations. When we send an email to the FM mailserver from MainServer we can see it on the server, we can see it in webmail, we can download it using a POP3 mail client. However, POP3it appears to ignore it like it doesn't exist. Any other emails coming from other mailservers are downloaded and added to the FM database just like normal.

Any ideas as to what might be causing this problem?

Here are the steps I've taken.

Rebooted the FM server.

Cleared and re-added the mail account using the POP3it Pro Server Config file.

Rebuilt the Mail folder on the mailserver.

Here is what the POP3it Pro CheckAccount Function returns even when there is a new message from MainServer in the account: Trouble Tickets checked; 0 new messages.

We are running POP3it Pro SE 4.1.9 which appears to be the most recent version.