My ML has the same setup, and I have two doors that are operated with the same brand garage door opener (with the rolling code feature).
Your problem may be the opener and not the coding sequence on the remote.
I know with some openers, they have a maximum allowable number of remotes they will recognize...after that, you need to reset the unit and start over (including your handheld units). Mine is something like seven for the limit.
When I first coded, I did one easily and but spent about an hour with the other...again, same units.
Find your owner's manual for the opener and look for specific instructions on coding. You have to sync up what you do for the MB remote with the "remote learn" sequence for the opener.
Antenna proximity may have something to do with this as well. I can't open the second opener until I'm close to the door because of the sharp angle of the driveway...
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2009 ML350 (106K) - Family vehicle
2001 CLK430 Cabriolet (80K) - Wife's car
2005 BMW 645CI (138K) - My daily driver
2016 Mustang (32K) - Daughter's car
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