Hi Juhana,
I see no reason why Patchage Muse & ZynAddSubFX woudln't work, make sure
you have the right connections in JACK MIDI (red cords in Patchage), also
check that the MIDI channel your sending in Muse is being responded to in
ZynAddSubFX.
I didn't test the mentioned stuff, because it will work if setup correctly.
Any other midi sequencer? Rosegarden failed to
install in Ubuntu (as well as GTK2 and SDL dev
packages grrrr!).
Sounds like an Ubuntu problem, perhaps contact the package maintainers of
the packages that won't work? Or have you mixed sources between eg Lucid
Karmic and Oneiric... That would explain such issues.
-Harry