Setting the instrument to MIDI Out Port: 2 (also regardless of MIDI Out Channel) looks like we don't get hanging notes.
That is indeed very strange. I really wish i had a newer version of LogicPro so that you can send me a project to look at it, because i just really think there must be something else that is being left out of this discussion, but its hard to guess just based on your description and not being able to inspect your problem project directly. I find it very odd that Port 1 out would not work and Port 2 would work. please make sure you are not using more than 127 tracks feeding a single VePro instance with AU3.
Also, when using any other MIDI Out Port besides 1, creating Aux tracks from the instrument track doesn't seem to work. Are Aux tracks created from the Instrument track in Logic (or vePro) not linked to the MIDI Out Port? And by Aux track, I'm talking about hitting the little (+) button on the Instrument track in the mixer. Not a huge fan of using Multi-Timbrel setups in Logic. I like the freedom to adjust individual instrument faders (unless there's a way to do that with multi-timbrel instruments I have overlooked without mucking about in the Environment).
Definitely do not mess around with AUX tracks right now. I really don't think those are going to work with AU3 at all.