On my M-300, the MAIN L has a different output level than MAIN R. Doesn't matter where I set the Master fader, the L and R are always different levels when they should be the same.

It's likely you have patched MAIN L and MAIN R to an INT FX port populated with the "P001 GEQ" effect. Please be aware this GEQ is a mono only effect; it will only effect the source patched to FX Source Left. FX Source right will have no GEQ. As a result, MAIN L and R are not the same output levels. To remedy this, recall P001 GEQ to FX1 and patch MAIN L to Source L. Then, recall Effect P001 GEQ to FX2 and patch MAIN R to the left Source of FX2. Then, link FX1 and FX2. Now you have two mono GEQ's, one for L and one for R. Since they are linked, any change you make to one will occur the other and the output levels will be the same.