If you map a key/button in the Pilot controls to jump to the CPG, you have to also map the key/button in CPG controls to jump back to Pilot seat. Not something as daft as that is it? Also if you've created a modifier in the Pilot Controls section and you and want to use it when you're the CPG, you'll need to create it again in the CPG controls section.
Sorry if I'm way off with this, but it's the first thing I thought of.
pixelpilot's post in Map Seat switch was marked as the answer