Check the center rail insulation everywhere. When you have run for a while, feel rail for heat, that's a tell-tale.
My thought is an intermediate(active when weighted), or micro short (close enough for larger "sparks of power" to "jump" the gap). The loco draw keeps the majority of power flowing properly, never shorting fully enough, or long enough, to ever trip the breaker.
Intermediate, and "gap" shorts, have a tendency to throw an offset into the ac wave too (which = a dc wave, which= whistles).
Broken wire(internally within insulation) can do this (dc) as well as connections (esp. where dis-similar metals connect and/or corrode.(like rusty pins on tubular, or aluminum connectors on steel/brass)
I could also see the serial signal getting interfered with should this be the case.
On the simple side sure, and I'm no command expert, but worth a look till better answers roll in.
I've had similar issues running tmcc (& pw) in conventional.
Also, newer Weavers only like one type of whistle control for sure. I thought it was "old school" pure sine wave, but I could have it backwards, they might like chopped.(the few I had? great creepers!)
Are your track & wheels really clean? Dirty track & wheels can sound electronics randomly all day.
Semi-related FYI, I have a mix of transformer & train brands/types ranging from pre-war to the 90's. The whistles/horns/bells, all act up differently depending on which transformer is used on which train. An AF 18b no whistle transformer is fine on PW, but modern sounds lose their minds on that unit (non-stop party time). My 4 1033's wont operate half the tmcc trains w/sounds. My new power units, wont operate PW trains well enough to "blow" any at all.