Same problem here. It was a total PITA, but it did finally take for mine. I have a Chamberlain Pro Liftmaster model with the purple learn button. Which is rolling security +, I think at 315Mhz. Anyway, hold the outside two button to clear the memory. Then hold in the button you want to program and the remote button to learn from at the same time. The blinking should change to a faster pace. No idea what makes this part happen. I must have done this step 50-100 times before it picked up my remote. After it picks up the signal, push the learn button on the garage opener. Then, push the visor button you programed. The garage opener light should flash and you will be done.
A good idea would be to unplug the opener while you are trying to learn the code. I didn't and the repeated attempts overheated the opener. It's also less anoying to not have the door opening and closing a million times.
Eventually, I was able to program both my garage doors. I still don't know what makes a difference. I didn't see any advantage to holding them both the 90 secs like they say it may take. Seems like the times it did finally take, it was in the first 15 seconds. I think it must be the newer frequency openers, because I had no problems with the same system on my Durango at my previous house with older Craftsman openers.