If you replace the 90 degree crossing with a straight track and the engine stops there must be a track issue where the center rail is not powered. The thread is so long and scattered I couldn't find if the locomotive did it in both directions at the same spot. In any case, if one truck is on regular track when it stops, it will most likely be the track, either no common in one of the rails, or no center rail power.
My guess is this has two dummy wheels, two rubber tired wheels, and two metal flanged wheels per truck leaving you just four wheels to make common ground contact and if two are on the plastic crossing you are left with just two. Without seeing an actual verified wiring diagram I'm not sure anyone can help. A blown TMCC Powermaster will pass full voltage no matter where the slide switch is.
