I'm having the same issue with my SL MkII and LPX. When you click on a plugin Automap assumes that your trying to tweak that plugin and switches to the Automapped control for that plugin (the light on the keyboard says FX or INST) The problem is that I can't figure out how to keep the mod wheel, pitchbend and expression pedal) working as their traditionally used (MIDI CC#1, PB, and CC#11 respectively)! Under global settings, you have the option to always keep the sustain pedal assigned to CC#64, why not the mod wheel & expression pedal?