I'm reviving an old thread here, but I just came across the same problem. I've found several similar topics posted (like this one:
http://forum.cakewalk.com...6348&high=MIDI+matrix) but no solution to the problem: Matrix works fine with MIDI files and soft synths, but as soon as I redirect my MIDI output to an external synth it goes silent ... How come hardware synths are not allowed?