I have been noticing this annoying issue with Cubase 6 and Cubase 6.5
I have a project with EWQL instruments and Reaktor and Padshop. I get all the volume levels to my liking, I export audio. I save the project. Good, good.
Next day I re-open the saved project, volume levels are different (The faders didn’t change, but the volume of each instrument has) sometimes I have to tap or move ever so slightly the fader and then BAM the instrument is back, sometimes I have to reload the VST instrument itself.
I have behavior that sounds like yours–except I’m using Vienna Symphonic.
Controllers in general (including volume) need to be ‘tapped’ to set them to the levels I want. I accomplish this by having an extra bar at the beginning of the piece, which begins with some OTHER automation value and ends with the values I REALLY want. It amounts to using automation to ‘tap’ all my automation/controller values.