Many thanks for the reply
According to Gametel, the controller uses the same
key-mappings as the Experia Play, which sends KEYCODE_BACK (I assume the same as the hardware back button) to the circle. When going to 'define hw buttons' I assume what's happening is FPSE just assumes that I'm actually pressing the back button, and does not set this to circle. So, what happens when pressing circle is exactly the same as pressing back on the phone.
In terms of config, I'm using the default other than turning off the overlay pad, and have also tried reinstalling/wiping data to go from scratch. The version listed is 0.11.29.
The only other comment would be that I'm not having the same problem with other emulators (e.g. SuperGsnes, the various oids and .emus), so there must be a way of working it. If I remember correctly one of them prompted 'do you want to set this key, or are you trying to go back?' to avoid this problem.
In terms of OpenGL, I tried switching to that, but it made no difference to the controller. Same for messing with pad 1/pad 2 settings. It's very frustrating, as FPSE is by far the best of the emulators out there, and is a perfect complement to a gamepad.