If the boards are both fed from rollers, and aren't sharing other connections, there shouldn't be an issue. That would prevent the two brands from running together period if that is the case.
I'd try lifting one of the Williams boards connections or whatever, and test the ERR board solo. Move to another power supply to test it also (I didn't even know Atlas made power supplies. If the design is chock full of electronics, chances are good that's the issue)... it should work on the Lionel supply; but just for fun which Lionel power supply? (some output differently than others)
A short on the track or in a car, etc. can also throw a dc offset into the mix. So can mixing some metals at contact joints (I dislike aluminum in electric connections because of this... it likes to mess with me.)
When you test, disconnect anything not involved with a test. In particular the power supplies. (not just off, disconnected)
A single led if not balanced by another led/diode can produce an offset too. Any singles added to the layout?
(I mention this because some folk recently have found some led that don't burn out on ac without reverse protection, and I bet folks are trying it... but that can create an offset too; an led is still a diode. Lay an 8a diode across your rails and listen to the whistle blow. Reverse it and you'll hear the bell..... hold it there and... you'll burn your fingers 😰 😏 😂...so use the other dyi button method threads to be serious about using them for dyi whistle/horn/bell. 
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