I was having similar issues and found that if I bring up a patch that does not involve Variax, then plug Variax into Helix via VDI cable, then press the Variax model knob in, then bring up a Variax-involved patch, I have no problems with Helix launching the originally-programmed models when switching through snapshots.
There were no instructions like that in the Helix manual, but for whatever reason this works for me.