iscorefilm, I believe you already understood what I'm going to explain. I used VI because the setup was simpler (one instance per staff), but Notion failed when handling a large number of instances. When switching to VE, setup becomes more work intensive, having to setup the extra staffs and assigning midi-channels for each, but the crashes went away.
Now what I'm failing to understand is why you are using the midi-outs to communicate with the VST. Are you opening VE as standalone and then routing the midi to it? This should not be necessary. In "Score Setup", instead of going to External MIDI, go to VST Instruments, and choose Vienna Ensemble.This will create a staff with a VE instance linked to it, then you can create the extra staffs and distribute the 16 midi-channels. Make sure that your ruleset is configure to "plugin" instead of "midi-out", the plugin ID for VE is 1448299589.