Ok ... I was playing around with mine yesterday and I see what you mean.

The problem seems to be that if MC-303 is not in Module mode, everything that comes in from midi cord (doesn't matter from what channel) gets played back from the channel you have selected from "Part select".

So ... to avoid this you need to filter out all the garbage (ie. all other midi messages except the rythm part.) You should (might?) be able to do this from Cakewalk Midi filter properties screen ....

Hope this helps a little ...