Good grief, I solved the problem. Battery. Even though my other fob had never been used, the battery was also bad (though no warning presented on the dash to replace battery like my other fob). Turns out you can test the fobs by pressing unlock or lock and there is a little red light that comes on for a second on the fob. If it doesn't, the battery is gone. Well, it didn't. Replaced the battery, light came on, windows go up and down via fob again.
Some complaints about the finicky-ness of this feature on the Mercedes forums.