My opener is model 139.53985DM. My remotes are: 139.53680 (which worked fine untils I tried to program remote 139.30498 (which I bought last year and it worked fine then, but I used it on another opener and it worked fine on it). When I try to program the remotes, the opener doesn't seem to recognize them, although I did get the newer remote to work after repeatedly pressing the control button when trying to program, but it only worked once when next to the opener and not thereafter. Reading the forum, it seems that my problem is probably with the logic board. I can purchase a new logic board from Sears for about $118, which seems silly when I can purchase a complete new opener for $159 (also seems silly when the opener was new in 2010). I could buy a logic board on ebay for about $65, but wonder if it might exhibit the same problems. Just not happy with the product at this point. Have purchased many Sears Craftsman and Kenmore products over the last 50 years and never had similar problems.
Check the connections both on the wall unit and in the opener itself. If one is loose it could cause this problem.
If its not the wires it could be the overhead opener itself, it could have something in it blown like a circuit.
I suggest you contact the manufacturer, they will walk you through fixing it on the phone most likely. I had a similar problem and they helped.