I'm running the latest version of RMX in Cubase SX3.01. I have a groove set up in multi mode so that one element is on track/channel 1 and the other element (from the same groove) is on track/channel 2. That's all good and well and works great. On the second element, I have set up some chaos parameters (quite a few) and the simplest way to punch them in and out of the song (as I don't want them on all the time) is to use the Chaos Designer's bypass/power switch. However, if I automate the use of the switch it appears to stay on all on the time on playback. The automation read mode for playback is enabled on RMX but it only automates individiual RMX parameters (knobs and sliders) not the bypass switch. This is the same for FX, it won't automate the bypass switch, only the FX knobs and sliders.
I do that all the time, so I can tell you it works. With buttons however, you have the problem of ambiguity about the initial state of the control at bar 1, so you may have to go to the automation track and draw in the first (on or off, whichever you want) data point at the beginning of the track. After that it should be ok.