Jump/fire and pause mapped the same on Xbox 360 controller

I am new to RetroArch so excuse me if this has been answered before :-).

I am running the 1.6 version on a Linx Vision tablet: http://www.linxvision.co.uk/. In short it is a Windows 10 Atom tablet with a Xbox 360 controller cradle. RetroArch works fine however I have a problem with configuring the controller.

The controller is recognized fine as an Xbox controller and works fine in the menus etc. However the B (and sometimes the A) button is somehow both mapped as fire/jump etc. AND pause in SNES games so that it alternates between pausing and firing/jumping. I have tried to change the input config but so far with no success.

Anybody else had this problem and found a solution?