As I often do when I'm stuck, I took a break last night and when I came back I had a fresh perspective and was able to figure it out. For the record, at least in Ableton Live 8.1, what happens is this:
I send a patch change command from my Motif or my M-Audio Axiom 61 on the midi channel for the appropriate Arturia VST I want to control. Each VST is on it's own track in Ableton with a specific MIDI channel mapped to that track. Ableton transparently passes patch change info through to the VST. The VST patch changes to the patch number within your currently active bank. It does not show up in Ableton's VST interface for that synth in Ableton's device view window (hey Arturia can you make this feature available to us Ableton users?), but the patch does change. I don't know about bank changes but if you disable the bank MSB/LSB messages and just send a straight patch number change (1-127) it should change the patch itself. The bank change commands may be what is preventing your patch changes. If the Novation lets you disable this then do so and give it another go with just the patch changes.
I was worried as I just spent the $400 on the Vintage collection, loaded into my laptop I use for gigging and when I couldn't figure out how to change patches remotely with midi. I was thinking "This is a deal breaker!" because I need this capability for live use. In the end though, it was a P.E.B.C.A.K. issue (P.E.B.C.A.K. = Problem Exists Between Chair And Keyboard)
Thanks Arturia for a killer product! I'm loving this collection!