Hmm, some quick testing here and I can't reproduce your problem.. My first inclination is your pan motor is having power connectivity issues, you might try a gentle 'pinch' of the motor's male connector, occasionally these barrel connectors can be a little out of spec and can loose connectivity in the center pin hole. By ever so slightly pinching the connector this will make it 'grip' the center pole on the MX3 side and make sure it doesn't loose connection..
Is there something in particular you're having a hard time understanding about setting up the rotary motor? Basically the only setting you need to set is the 'motor preset' under the axis your rotary motor is connected.. There's not much more to it, but perhaps I'm missing something? We're available during business hours via phone and virtually 24/7 via email at firstname.lastname@example.org if there's something that's not making sense to you..
Understand that your not setting 'Aux A' to flip direction.. your setting I/O 1 to flip direction.. You have 2 I/O lines per Aux input. (Aux A = I/O 1 and 2 -- Aux B = I/O 3 and 4)