The TIU takes a few seconds to power-on during which time power would flow through the fixed channels, along with a watchdog signal. However, there may be a delay in turning on the variable channels, since they, unlike the fixed channels which are wired straight through the TIU, have to turn on the circuitry that allows power to go through he variable channels.
Even if the variable channels are set to fixed mode, it's entirely possible that there could be a delay before they, too, can pass power. If I had to take an educated guess, I'd guess that this is normal TIU behavior that previously went unnoticed.
Regardless, the watchdog signal is sent out for 5 seconds on each channel, independently, only after power appears at the channel output, so that this delay is extremely unlikely to be the source of your engines coming up in conventional mode.
You say that previously you did some wiring work that went somewhat awry. I suspect that this is closely related to the engines starting in conventional mode, and that the 5 second delay has always been present.