I have connected my Rtym to my drum kit and on one occasion when I was playing along to a pattern it mysteriously set all the velocities to zero for all of the trigs on one track, but not on the tracks that were being fired by the drum kit. It was very strange and I am sure it is a bug. Have you tried checking if the velocities of the silenced trigs have been set to zero?

But my more burning question is: why would you want to connect a Rytm to a computer? Surely the point of owning one is that it sets you free from a computer. Otherwise, there are plenty of software synthesizers and drum synthesizers that are much cheaper than a Rytm.

The reason I play it with a drum kit sometimes is that having some live drumming in a stage performance would liven it up a bit for the audience.