run the engines uncoupled and a few inches apart. See if the speed is a big difference between the 2. Sounds like one engine has binding issues.
I have not had this issue myself. Usually when matched, they run well in both directions. I did have a G scale engine with loose motor mount screws. That caused the gears to slip. It made an audible clicking sound, more so in one direction.
Look at the traction tires if 3 rail.
