My best try.
Hi John,
I feel sorry that no one responded to you yet.
I did read your post twice trying to figure out how I could help you, and I did not found any simple avenue.
I really thought that by now someone else would have come to the rescue...
I'll shoot what I think anyway.
Is the problem seems to originate from the remote control, or the trigger(s)?
Could you describe in other words when the problem first surfaced and what caused this new behavior.
Is your Rotel RC1082 pre-amp working fine by itself?
Can a delay be apply to the trigger(s)? That might be the problem.
The connections for the triggers should well be explained in your manual.
(Like you said, the OUT goes to the IN of the other component.)
Maybe you need a power conditioner with adjustable timers on the AC receptacles?
Also your Logitech Harmony ONE remote control has a delay feature that turns your components ON and OFF at different times.
That's my best shot so far.
Regards,
Bob