For the Berk, try a conventional reset, which cannot be done with a DCS signal on the track or with a remote.
When you stay "automatically start," I assume you mean they start up, not that they take off.
I have many locos on powered tracks when I start up, and have never experienced any issues.
You are aware, I expect, that the watchdog is only sent when power is applied to the TIU input, not when you turn up the voltage.
I am using 4 Variable channels, all set to fixed. Two are fed from an ancient ZW whose handles are left up. Two are fed from a PH180. No issues.
Be sure that all of your TIU black outputs are wired together, preferably right on the TIU with a jumper. Do you have enough ground feeds to the outside rails?