I would look at an intermittant contact in something that sends a signal. When I crfawled inside to sove the parts catcher mystery for myself, I found the electrical connector plug on both coils that fire the solenoid had been installed, but not secured by the allen screw that locks them in place. After tightening the hardware, the probelm went away and I haven't seen it since. I'm not sure if it was the factory or one of the 3 or 4 guys they sent to troubleshoot the problem that forgot the screws.
The ATC isn't a great mystery. There is a lot going on, and the machine checks for confirmation of various states before moving on to the next part of the sequence. If the confirmation isn't sent or received, the sequence halts, waitng for an update. If it quits with the changer and arm on the side that allows a tool change, the next tool change sequence will work if the signal is re-established. If something is out of position you will get an alarm.
If it happens on the first part, are you running in single block? Single block won't allow a complete tool change and you will get a cycle timer over (or similar alarm) or the machine will just sit there... is the green light on the start button on or off when the tool changer hangs up? Hitting reset in the middle of a tool change is a bad idea also.