Confused about transposition and concert key.

I'm transcribing "Venus, the Bringer of Peace", which has a key of C minor, and the Bb Clarinets are shown on the score in the key of D minor.
I have tried switching between "Concert Tuning" and "Concert Pitch" and even played around with the track settings, but nothing seems to fix them.
They play back (as you might expect) a Major Second higher than they should (and sound utterly dischordant, and if I manually drag them down a Major Second they sound fine) and I don't know what setting I need to change to fix it. Coming from a digital music background, I'm somewhat new to concert pitch and transpositions.
I've looked at sections 3.7 and 8.3 in the manual, but I'm still confused. Changing the transpose values in the Track Setup (on the second tab) doesn't seem to make any difference?? The octave updates if you change that, but not the other A-G options?
Any help from the orchestrally savvy would be much appreciated.
I have tried switching between "Concert Tuning" and "Concert Pitch" and even played around with the track settings, but nothing seems to fix them.
They play back (as you might expect) a Major Second higher than they should (and sound utterly dischordant, and if I manually drag them down a Major Second they sound fine) and I don't know what setting I need to change to fix it. Coming from a digital music background, I'm somewhat new to concert pitch and transpositions.
I've looked at sections 3.7 and 8.3 in the manual, but I'm still confused. Changing the transpose values in the Track Setup (on the second tab) doesn't seem to make any difference?? The octave updates if you change that, but not the other A-G options?
Any help from the orchestrally savvy would be much appreciated.