Hi,
It sounds like the weird stuff that is happening is the default FS functions for the key combinations your buttons on the fmc are currently mapped to.
Just done a quick google (other search engines are available) and it looks a little bit like you can not map into the pmdg fmc, that is probably the reason why engravity had a specific interface application for their fmc to pmdg...
Not familiar with the fmc you have but I wonder if it would be possible to get an OC key card and run the pmdg fmc in its own window, i know with the OC key card and sioc you can assign which window the key presses go into and looking at Ian's site he maybe got something going with the OC card and using fsuipc mouse macros... http://www.737ng.co.uk/opencockpits.htm bottom of the page on the right...

Cheers
Mike