One of your remotes has reverted to an earlier technology. (manufacturers explanation) What you need to do is purchase a new remote. Make sure it is the exact same model number as your original remotes or guaranteed compatible. Then you will find you can program it and one of the old remotes. A process of elimination will show you which is the bad remote. Remove the batteries and toss it so you don't have problems with it in the future.

I'm not quite sure I understand. Both of the remotes came with this unit new. The outdoor keypad, I just recently purchased in hopes of using because I couldn't get both the factory remotes to work at the same time. Since the keypad is new, shouldn't that have resolved any programming issues? Sorry if I am misunderstanding you. Thanks for the reply!

What makes it difficult to understand is that they still work but won't work with one another. Trust me, buy a new remote and you will find you now have two that will work together. Throw the other one away.

Throw the whole Craftsman opener away and get a Genie.... or keep the Craftsman and come back here to repair the thing about 2 dozen times...then you will chunk the thing.