Thanks guys for your quick replies!
Paul, you were certainly on the right track and Al, following your procedures worked perfectly. Renamed the .pro file, restarted and now all buttons work without the need to open the MS Controllers window.
This issue did only pop its head up after manually creating offsets and compound buttons for the mode switch positions, what I was noticing in FSUIPC however was that when trying to figure out each button number, FSUIPC would recognize the mode position first press of the button and then the actual button on the second press.
After applying this fix that doesn't occur anymore.
Happy Days!! now onto the PMDG assignments....