Re-learn the command as many times as you can (create a bunch of dummy buttons) ...

1. When you learn, use "learn-1" for some and then use "learn-2" for the others
2. Learn it by quickly "tapping" the button once to learn, then again by pressing and holding, then again by repeatedly tapping
3. Learn the code with the remote pointing right at the MX-3000 for some, but for others "pull" the remote away while you're learning

When you are done you'll have 10 or so versions of the same code...download and test each one to see which (if any) behave the way you need it to. If not, I personally would repeat the steps above knowing that eventually it should learn properly.

I know it all sounds silly but it gets around the problem with checking/unchecking the "repeat while button is pressed" box (which never ever seems to work for us). Thanksfully most codes learn fine or are in the database, but every now and then when you get a tricky code like this you'll just have to play around with.