Sounds like you could be hitting CSCae05933. By default in 3.1(3) you can still run into the situation where messages are "backed up" in the \commserver\UnityMTA directory. If you go look in that directory, I'll be you see a bunch of messages in there. The release notes for the above bug have the work around for this:
CSV import of subscribers may contain spaces after the last name or first
name. Where the example "Last ,First ,1234" shows spaces after First and
Last names when the following is expected "Last,First,1234"
Messages in the MTA directory may not all have the condition. Only one
message with the condition will cause all others to remain in the UnityMTA
without delivery. See workarounds below.
To correct the CSV files before import, find and replace any string like
" ," (no quotes) with "," (no quotes).
If subscribers have been imported and message delivery is failing:
If you are running Unity 3.0(4) or Unity 3.1(3), you can add a registry key to
the automatic moving of blocking messages to a specified directory for
To enable this do the following (assumes Unity is installed on C:, modify the
drive letter as needed):
1) Stop AvUmrSyncSvr service
2) Create a directory called Failed in c:\Commserver\unityMTA
3) Run regedit and add the following registry key:
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