I've been having exactly the same problem as you with locos not stopping on DCC if they'd been running for a few seconds. Definitely decoder related in my case, tried two Digitrax Dz126INs and a Gaugemaster one, all do the same problem. Tried every CV setting under the sun, eventually relegated all the decoders to function only and they're fine!
Not teaching you to suck eggs, but I'd definitely either try one of the decoders in another loco, or try another decoder (again) in the problem locos!