I am having an identical problem with the Mulitport Layer.  I am getting errant MIDI data going to seemingly random instruments that are within the same VEP instance (I only have one in the sequence).  Not only does this happen with MIDI volume moves while the sequencer is playing/recording, it also seems to happen when I option drag objects in logic to copy and paste them while Logic is playing.  Man, I just spent quite a long time setting up a VEP template and now I can see it's going to be trouble.

I noticed that with my recent purchase of VEP 5, there is a Logic file that comes with the download package called "VEP Multiport Layer.logic"  

Is this the only way in Logic to access multiple MIDI ports on one instance of VEP?  This seems kind of clunky to me.  I was using Plogue Bidule before and those MIDI ports showed up automatically in Logic so for every multi-timbral instrument I could easily assign a descrete port and MIDI channel.  

Is there not some simple way to do this with VEP and Logic?  

Any tips would be highly welcome.