Hello, I'm having a very similar problem with some Alchemy presets. Specifically: put two Alchemy presets in a certain Mainstage set, say "am I funk" and "bad habit". Now in Mainstage's patch list i switch to the first patch - sounds well - but if I go back to the second patch ("bad habit") it sounds completely messed up, so I need to change the preset in Alchemy window then go back to "bad habit" for getting the right sound again. I made some tries, including disconnect of all midi devices but nothing worked...
Tried to create to tracks in Logic with the same two presets, and I'm not having the same problem instead.