I don't know if this helps at all but I've found someone else with a similar to identical problem using the same OS versions as me but with a different model (Q5 instead of Q10).
They use http://www.zarafa.com/
Update: The same user using the above product reports the exact same syncing bug you fixed/worked around in the custom build. They also would set a sync interval on their phone and all sent items would sync. Doesn't look like the issue is specific to your implementation of ActiveSync and might be a bug in Blackberrys device that doesn't happen on a Microsoft ActiveSync server.
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