Billbarman,
I have an Atlas RS-1 of the same generation as yours and had the same problems with it. Stuttering at low speeds and seemingly working OK after running it a while. It is equipped with EOB. It's not an EOB problem, its a power pickup problem.
I contacted Atlas when I first got the engine and Bill S. told me they had found something wrong with how the wheels were made which caused them to have power conductivity problems between the wheels and the outside rails. Their solution was to clean the wheels and then apply their conductive lubricant to the wheel tread. I did that and it helped, however it didn't take long for that lubricant to wear off and the stuttering problem returned.
Some years later I bought an Atlas dummy SD35 which came with an extra geared wheelset (I guess in case you ever wanted to power the unit). I installed that wheelset and transplanted another wheelset from the SD35 into each truck of the RS-1. Again the stuttering problem improved but I still had problems with power dropouts going through some Atlas switches and through somewhat dirty track.
Some years later again I found a junker later production RS-1 with two pickup rollers on each truck. This time I transplanted the trucks off the junker to my older RS-1. Problem fixed! The engine runs reliably at low speeds with no warmup running and no stuttering.
So my solution was to replace the original trucks with ones from a later production engine with extra pickup rollers. Not a very practical or easy answer to the issue. Getting the newer trucks would be difficult and actual work involved replacing them is not easy and would require another long explanation. The RS-1 has got to be the most difficult to work on engine I've ever encountered and mine has been a lemon until relatively recently. If you want a recommendation from me, it would be to sell it and if MTH made an RS-1 in the roadname you want, buy that.
Ken