[akm2018]

I run large orchestral templates in Pro Tools for scoring to picture. I mostly have Instrument tracks routed to VEPro, one track per patch, with MIDI going to VE and audio from the patch in VE routed back to it's corresponding instrument track (the same one the MIDI was sent from).

I personally don't have any issues with my setup, either with midi notes or controller data not being played back correctly. This makes me think that Mind Control might be the issue. Have you tried taking Mind Control out of the equation and seeing if you get the same or different results?