This may be dumb, but I'm accustomed to setting a transposition for each midi track in sonar 5, can't find the same thing in X3?   For instance, Bb clarinets get a -2 transpose, double basses a -12 transpose, both in half steps, so that the piano roll and event list and all show the pitches the way the score shows them. 
 

In the track inspector, key and time offsets pointed to by "P" below

Ah, thank you.  I usually close 'track inspector' because it takes up too much space, but there's a reason to open it once at the beginning of a setup.