Since these locos all worked well before, and the are now pushing 20 years old, I would be much more inclined to suspect the motors before messing with the back emf settings. 20 years is a long time for an N Scale motor, if you've been using these engines regularly over those 20 years. You can pick up the eBay replacement Atlas/Kato motors really cheap off eBay these days, even though you may find that 2 or 3 out of every 10 don't run very well. Sometimes, they ALL run okay. It's not as reliable as paying retail and buying new motors, but then, these are selling for $1.50 to $2.00 a piece.
I guess the first two things I would do:
1. clean out the commutator slots in 3 motors in consist and see if they work better
2. blindly put new motors in the three engines and see if the problem goes away.
But I think eliminating worn motors is the first step in this diagnosis.
Are you able to hook an ammeter into your power supply and see if the current climbs as you run the engines, to a much higher level by the 20 minute mark? That would be another indicator of motor problems.