On further investigation a number of CD32 game have this issue, sometimes requiring port 1 and sometimes port 0. Individual settings files looks like the solution.
Generally CD32 games like a CD32 pad in port 1. The following games are exceptions:
Fire + Ice CD32. Needs a joystick (not a pad) in port 1.
Seek and Destroy CD32. Needs a CD32 pad in port 0.