The instructions are pretty vague on flight plan/auto pilot operation

What aircraft are you flying? If your aircraft does not have the MS standard auto-pilot our co-pilot can't fly it. Some examples are PSS aircraft and PMDG series aircraft.

The last two flights were Flight 1 ATR-72-500 and the FFX/SGA DC10 Series 30ER

Do those two aircraft utilize the MS auto-pilot technology or do they have thier own proprietary routines? I don't know. Maybe someone else can chime in.

As I understand it the F1 ATR has it's own autopilot interface.Rule of thumb: If it has a NAV mode not running off the default GPS or if it has 'fancy' modes such as pitch controlled IAS hold then it probably aint default...Can't comment on the DC-10 as I don't know what panel our friend is using with it.

I'll experiment with other planes

Yes you are correct. Any of the Flight Sim default aircraft work correctly with our co-pilot. If they do the same thing as you have been experiencing then it is something else causing the problem and we will pursue it from there.