I found that a few connections in the simulink model of c1scx was incorrect, so I fixed them correctly.
It had been a mystery why we had to put a funny matrix on ETMX (see this entry).
But now we don't have to do such a voodoo magic because the problem was solved.
Now the damping of ETMX is happily running with an ordinary output matrix.
I looked at the wiring diagram of the ETMX suspension (it's on Ben's web page) and confirmed that the coils are arranged in order of UL, LL, UR, LR.
But then I realized that in our simulink model they had been arranged in order of UL, UR, LL, LR.
So UR and LL had been swapped incorrectly !
So I just disconnected and plugged them into the right outputs in the simulink model.
I rebooted c1iscex in order to reactivate c1scx front end code.
After rebooting it, I changed the output matrix to the usual one, then everything looked okay.
(actually it's been okay because of the combination of the wrong connections and the funny matrix).