When you initially activate the CNC12 software, it really just enables the axis as you try to jog them. So it will really just enable the system once all the axes are active. All the axes will be enabled once you try to run a g-code, home the machine or do a full activation of the system.
To prevent this you should enable the system and all the axes at once.
We are working on new revisions of these boards that will handle this better by making sure all the axes are enabled together. The new boards should become available before the end of this year.