Let's call these garage doors number one and number two. I think what you did was program one of the remotes from number one to number two or vice versa. This will cause that problem. What causes confusion is you are not programming the remote, you are teaching the receiver to accept the code from the remote. Now then what we need to do is go to each motor unit and hold the learn/smart button in for six seconds. This will erase the memory of both units and none of your remotes should work. Take the remote(s) you want to work with number one and press the button on the remote while you press and immediately release the learn/smart button on the motor unit. Do this for each remote you want to operate number one. Now do the same thing for number two. You should be okay.

Your hand held remote needs to be replaced and they both will work. The intermittent problem is anyones guess. If the unit is over 10 years old I would replace it.

There are two completely separate possible problems. Problem #1 is a noisy LED (not, sound noise, but electrical noise that makes radio interference) that makes it more difficult for the radio signal from remote to base to work. Problem #2 is a capacitor on the board that wears out with age that affects the wireless capabilities. The LED bulb doesn't cause a bad capacitor or vice versa. These are cumulative issues, but unrelated in cause. So, it's slightly possible that a combination of these two issues could exist where the cumulative effects of both are enough to make it not work. But, one doesn't cause the other. Test #1 is to just temporarily remove any bulbs from the opener and see if that makes a difference in how the wireless remote works. If it does, then you probably just need a better bulb. If it doesn't, then the next most likely cause is the capacitor. For my opener, the bulbs made no difference. Mine was fixed by replacing the capacitor and is now working fine (at 25 years old).

I asked the sales person at Sears and they said that you would have to buy a new 3 function remote if the numbers are not compatible with the openers. They said I could go online to find out if each are compatible with each other but I have yet to find the website to show me the compatability ability. Sears should state on the new openers that they are not compatible with older remotes before you buy. Or tell you to bring in your info on your vehicles and your old remotes and replace them for your or at least let you get something towards a trade in value.