Ah yeah - I'm afraid that the Atcyclotron is still yet to be updated to the Version 2 libraries (which has the normal MIDI channel change). Unfortunately it doesn't have MIDI channel change at the moment. I'm definitely going to update it soon though!
Atmegatron and Odytron currently use v2 libraries. Atcyclotron, Delayertron, Duotron and Atmegadrum are still waiting to be updated.
However.... Delayertron and Duotron have a temporary fix for MIDI channel. If you go to the MIDI tab in the Arduino sketch, about 40 lines down you will see byte MIDI_channel=0; Change this to any value you want and then upload the software again.
Hopefully I'll have all software versions up to date by summer (it's quite a big job!).