This is a controller configuration file problem. It will be fixed in the next release which should be tonight. However, if you see this happen again, it is an easy fix that you can do. Just click on the controller in the left hand pane, then click on the configure controller button right next to the - sign above the controller list. Make sure the number of channels matches what the controller shoud have then click ok. You will need to do this with each controller that you want to use that is having problems. Thanks for bringing it to our attention.
Ryan