OK, two things come to mind:

1. The simplest explanation would be a loose orange wire in any one of the towers. On the post-2000 Zimmatics, all wires that don't have something to do in the intermediate towers are nonetheless junctioned in each tower box on that rotary switch and the barrier terminal. Check every intermediate tower to insure your orange wire is carried through successfully.

2. OK, now the more complicated. In the second-to-last tower, the percent timer line is run through the stall timer. This will be a little blue box with a dial on it. The way this works is that if the last tower has been running for > 90 seconds (factory setting), but the second-to-last tower hasn't kicked on in that time, then the stall timer opens up the brown lead and safety-stops the machine. If the last tower has been running non-stop for 90 seconds and the second-to-last tower hasn't had to come on in that time, then the end tower is stuck. Someone could have mucked about with the stall timer -- they're just a little box with a dial on it, and nothing in the manual to say "Set this to X, and LEAVE IT ALONE." The old manuals said that, but the new manuals all say "Call your dealer" for everything. Fat chance when the nearest dealer is 240 miles away.

3. Last issue: If this problem only happens in one direction, there's a "turn-around" relay in the last tower that turns the voltage on the forward/backward lines (purple/pink) back inward on the machine, down the brown line. This relay is a SPST and I think the forward is the normally closed setting on it. It's just a wee little relay, an insubstantial little poof of a relay. If you had a lightning hit or some other problem, it could be burned a bit and be intermittent on the energized setting, which would make the brown lead open up, stopping the machine. The best way to determine if this is the problem is if the machine has problems only in one direction and not the other.

The best way I've learned to think about how pivots operate is this: the end tower moves. The rest of the machine plays catch-up. Nothing happens until the end tower moves far enough to cause the next tower inwards (the second-to-last) to see the alignment switch get far enough out to cause the second-to-last tower to move to catch up to the end tower and keep the machine in alignment. So I go looking for problems from the end tower inwards now, rather than the pivot panel outwards.

If you need the schematic, just yell. I've got nice, clear copies.

I also have the data sheets on the stall timer.