..but wait.. you may be my lucky charm Steve!
Just tried starting again, same clicking from alternator, again failed to stay ticking over, repeated, repeated, then no ticking noise and she starts, so this looks like it may not be Commander related.
Can anyone confirm that plugging a Commander in to an Apexi FC and viewing only in monitor mode, cannot break or reset anything? This will help me trouble shoot.
The noise, combined with the frequency at which I recharge my car makes me think that perhaps it is time for a new alternator..any thoughts anyone?