I believe I did get the glitch fixed—at least it is so minimal now it shouldn't matter. It's odd. Kevin Price suggested taking the gears off and running the motor, and maybe switching the motor, to see where it was finally coming from. Well, when I ran the motor alone outside the tray—no glitch what so ever. Then I dropped the motor onto the tray and part of the hull while it was running, and the buzz and vibration made the APC go nuts. So then I touched the running motor just to the tray, and it happened again. So the culprit was just vibration from the motor and metal gears being transmitted through the tray.
I got a pair of plastic gears and tried to isolate the tray from the motor and end cap it is attached to as much as possible. Kind of like the real boats how the decks are free-floating and cushioned from the hull for sound reduction, I used rubber bushings where the tray attached and touched the end cap. And now it works really well.
Thanks for all of the response and suggestions on getting rid of that glitching, all. I've not heard of it NOT being caused by electronics, so this was just a fluke that I found out it was vibration.
I had the whole boat ready to go together last week, and then when I tried to turn the lights on—ZAP, FLASH, SMOKE! What the heck! I quickly turned the whole thing off. Upon inspection, all of the wires going to the lights were hanging bare, with the insulation dangling off in all kinds of places. Turns out, the little (probably 30 guage) wires to the tiny LED I had up on the periscope mast fairing, must have gotten knicked. THey only had something like varnish coating on them, like motor winding wire, and they short circuited. Blew out the "S" light circuit that was attached to it (that's where the flash and smoke came from). So once I get a new circuit, coat the new tiny wires with shrink coating to protect them, I should be ready for a spring run soon.