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.
All current C86ACORN and C86ACCP boards enable when they receive the axis enable signal for any axis from the ACORN.