Thanks for the link wetriner - wish I had checked this earlier as I was able to resolve it just before checking the forum!
The method I followed appears slightly different. It took going to to the "/configs/all" directory editing the autoconfig.cfg file. Changed the setting on the the "mupen64plus_hotkeys" from 1 to 0. And then going to the mupen64plus.cfg file and changing the "joy mapping stop" to "J0B10". Ensuring to save the both files before exiting. I again was required to use the command lines as the file would not save remotely from windows.
I nearly have my controller working 100% across all emulators except for Dreamcast - just cannot find a solution to get trigger buttons working. :(