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Sounds like the rails are not in sync between the mainlines. Try switching The Rail A and Rail B wires on either the DCS 240+ or the DB 220 but not both.
Are the Command station and booster grounded together?
I don't have either of the units - 1) Make sure you have a ground wire between the command station and the booster2) Make sure the booster is not set to be a command station3) You said you have one run the entire layout with one unit .. that seems to imply that you don't have any separation between the two "tracks" or "power districts" .. it would help to see a track diagram with your power districts laid out
You might not need to run the entire layout with two boosters .. One other thing to test .. put a continuity tester between the rails of the east bound main and the west bound main .. (same track to same track) .. if you get a sound .. then you probably have a cross connect between the tracks and the boosters are working together A ___________B____________A____________B_____________Measure A to A, B to B
Good to hear Nate .. That's a good solution .. but it's worth while to still troubleshoot the issue .. One quick test with your new configuration. Disconnect one of the two power district cables from the DB220 and see if trains will still run on both mainlines .. that should tell you if there is a possible interconnect between the two .. I've on occasion mixed up my power drops when wiring up the layout . .Good luck