How are you controlling the engines? Manual throttle, Legacy, Bluetooth with a handheld device and app?
If you have identified troublesome areas, just exchange a piece or two of track from that area with another area, particularly 10" pieces.
A lighted caboose or passenger car is handy to roll around and check for good power. Remove any other cars or engines.
If you are using a Legacy base, try connecting the base track wire to the Black output terminal on the transformer.
