When using the Cyber Commander/CSXCV or, to a lesser extent (due to less control available), Pocket Wizard TT/MC2 any input from the control panel on the light itself is overridden by the transmitting device.
There is an option in the TT1/TT5 menu in the PW utility for model lamp control. If it is enabled, then it will override flash unit settings.
For specifics or further assistance on the MC2 or any other PocketWizard product, please contact LPA (PocketWizard) at
http://www.pocketwizard.com/contact/inquiry/,
info@pocketwizard.com or 802-658-0038 x572