This is probably a really easy one, but I really don't know the answer.
I work almost exclusively with Cubase and have noticed, with Trilogy only, that previously sequenced bass lines that work fine playing through on a GM sound on a Motif, that they seem to transpose lower on Trilogy.
I have had that issue as well. Usually, when I import a GM bass part into DP with Trilogy, I edit out all of the controller information. I sometimes have to transpose the bass line up an octave. But other than that, no problems.