Something to try: When you hooked the switch up to accessory power, you had to remove a jumper pin that ties the track (center rail) to the switch motor power. After removing this jumper, you are left with one screw terminal that can now be used to power the center rail of the switch. Run a wire from the hot side of your track power to that remaining terminal, your switch is now a power lock-on. Run your engine through the switch to see if that solves your problem.
See the image below for reference:
This may or may not solve the problem but you'll know positively the center rail of your switch is powered. It could also be just how the center pickup rollers find the brief "dead" spots in the switch.
