Fair enough - that's the first obvious hurdle out the way
Reading your post again, you say you called up selected flights after pressing ProPilot...
You need to start with FS actually running a flight first with the engines shut down and
then press ProPilot as then the Flight Logger will send the information to FS to switch plane and location to match your locked flight. So as soon as you switch windows back to FS, you should be ready to fly!
To make doubly sure, I always load up FS at the right airport and gate with the right plane and then shut down engines before doing the Flight Logger bit then nothing can go wrong
Good luck!