Phil: It may not be the cause of the stuttering / intermittant operation you have described, but it is always a good idea to check that when the NMRA plug is pushed into the NMRA socket, that the pins don't touch and short together on any metalwork beneath the socket! It may seem obvious, but I had this problem on one ogf my installations - and if it happens in only one direction, or when the lights have been turned on (not obvious if none have actually been installed) - that a 'positive' is suddenly in contact with a 'negative' (which in the other direction was positive or floating).. and that the decoder module is protecting itself by current limiting ot shutting down intermittantly.
Solution: If you cannot see below the socket that the pins are NOT exrending to metalwork, uncsrew the socket, add a small piece of insulating tape to the metal chassis below, and then refit the socket.
Also, ((but not common with UK stock)) check that the decoder cannot come into contact with a metal body (OR metal parts of 'handrails' or similar fittings which pass through the body) when it is refitted. (I took the precaution of insulating-taping the inside of a Trix loco body recently for that reason.)
ALSO: check 'unused' wires: eg the violet wire on the 4-output decoder if not actially being used should be INSULATED at the end - as should any other 'loose' wires - and in a way so that they cannot touch each other in later life (eg trim bare end off, and then insulate with gapes between them) - keep them a usable length in case you add lighting in the future!