*Temporary Fix *
Well I finally got to the bottom of this. Amiberry does not register when button 15 (select) or 16 (xbox) are pressed on an Xbox One 2016 Bluetooth pad (maybe some other Xbox pads as well). The short term solution is to assign the Hotkey to another button that is not used in Amiga emulation e.g. 14 (right analogue press).
Is it possible to make a dedicated Amiberry joypad config file in Retorarch that only Amiberry will pick up on. While I'm at it could I do the same for other emulators such as LR PCSX Rearmed?
Thanks to Horaceandthespider at Github for help in resolving this.