OK, doesn't seem like anyone else has this kind of problem, but I solved it and it might help someone in future if I describe the solution.
I have bars orientated vertically on the right hand side of the screen with empty action slots hidden and collapsed. Without these options, the minimap would be partially covered by the action bar, and so some of the buttons on the minimap are in effect covered up, even though the bar is collapsed. Solution is to ensure that the full uncollapsed action bar does not cover the minimap