Your problem is remembering me problems I had when I develop my environment.
If you want to send me a song with just a few notes on a few midi port and on a few midi channel that is causing you problem I can monitor the result and if It is the problems I had I could give you a fix for the environnement
Just cross fingers
[UPDATE]
For the sake of tying up loose ends, I've just been testing Logic 10.7.2 with and without the VEPro AU2 plugin, while still using VSL's multiport AU2 multiport workaround - also testing the snake oil 3rd party revision of VSL's AU2 workaround.
The good news for VSL is that the VEPro AU2 plugin appears to be innocent! Logic 10.7.2's Environment still produces its spurious garbage even without any VSL plugin!
The problem appears to be that the Transformer object in Logic's Environment is currently very badly broken. I discovered this by sending the output of VSL's AU2 multiport workaround addition in the Environment directly out on an IAC Bus, then examining what appeared on that IAC Bus in Snoize's excellent MIDI Monitor app. Logic's spurious garbage is there in all its glory in MIDI Monitor - with no VSL plugins in the Logic project at all! The snake oil revision of VSL's AU2 workaround, as expected, sends out the same garbage as VSL's version.
There doesn't appear to be any way of testing new Logic's multiport behaviour without the VEPro AU3 plugin, so at present I'm unable to demonstrate the guilt or innocence of the VEPro AU3 plugin in Logic 10.7.2.
Although it's no help to users of large templates in Logic, VEPro AU2 still appears to work normally in new Logic on a 1 Instance with 1 port per VEPro plugin basis - i.e. without the extra stuff in Logic's Environment as required for VSL's AU2 multiport workaround.