Thanks for the reply.
I've read the manual and did all the settings i needed to do.
The main outs were indeed set to 3-4 on the front panel in control room options. but still for some reason unknown linux keeps playing them through 1-2 & ADAT2 1-2.
I also saved my routings on windows into the unit setup (1-6) on slot one, and loaded it via the front panel, again, it keeps playing the audio through output 1-2 totally ignoring my settings.
Seems like linux is overriding the front panel settings.
I guess i'm out of options?