I'm having the same midi problems as Wolfsterik.
I'm using a Mac Pro 8-core and Logic 9.02 as my Master DAW (OS 10.5.8) and two MacBook Pros (OS 10.6.1) as slaves using VE-Pro's 32 bit server - the 64 bit ones wouldn't give me the option of loading any of my AUs (Kontakt 3.5, Omnisphere, RMX etc) for some reason. Anyway, I digress, the midi irtregularities happened with the first version of VE-Pro and unfortunately are still occuring with the update.
I created a Logic template of 8 LASS Instruments (8 midi channels) on one slave withiin one instance of VE-Pro. All worked well until I relaunched the project. Midi channels 1 - 4 and 7 - 8 play fine. 5 and 6 are problematic. Even though I can see that they're being triggered by the VE-Pro's track light on the left, there's no sound. When I then click the Kontakt's keyboard with the mouse on the slave it plays, it just doesn't when being triggered from my main DAW.
The weird thing is that on the last launch of the project, midi channels 5 and 6 didn't play. On the current launch, 5 does, it's 6 that doesn't. By the way I've tried this with other AUs and the same thing happens. RMX, Omnisphere and other Kontakt instruments are also problematic.
Nick
Edit: I've just tried deleting the problematic AU channel on the slave (Midi channel 6 at the moment) and have loaded up an Omnisphere instrument on 6 instead. It works fine. I then deleted the Omnisphere channel and freshly loaded up Kontakt on MIDI channel 6 and nothing sounded again (even though it was clearly being triggered and DID sound when triggered by mouse on the plug-in's keyboard). It was just a regular factory preset I loaded too - nothing very intensive. Bizarre...