Thanks for the tip. I started counting and currently have 6 potential remotes including my Atlas: both original remotes, the Homelink on my wife's Infiniti, a door status indicator with closer button in the kitchen, and probably the Homelink on my previous vehicle (silly me, I forgot to clear it before trading it in). Wondering if one of the other remotes causes the Atlas to get kicked out of the main unit's memory.
Also, something I neglected to do is perform the last step in programming by syncing with the main unit. Guess I should have read the manual a little farther. I did see something about it on Chamberlain's website, and my wife found this handy YouTube video:
Anyway, will try reprogramming/syncing per the manual and see if that sticks. Otherwise I may have to reset the main unit and reprogram everything per hfqkhal's suggestion.