EIG actually should be counted, because Jim Henson Pictures was involved with production along with CTW (as opposed to FTB, which was produced by CTW only): Brian was even executive producer.
Both The Dark Crystal and Labyrinth could be counted as well, but they can't because they truly are separate entities as Jim wanted these movies as departures from his traditional Muppet fare.
EDIT: I think another reason why MC is declaring the new movie as the "seventh" is because it seems like the Muppet community, as a whole, likes to pretend that KSY and MWoO never existed... yet they always praise IAVMMCM... and you know what? If Jason Segel ruins the new movie with his filthy sense of humor, I might have a chance of removing my personal "Worst Muppet Movie to Date" title from IAVMMCM, which... I don't know, it seems like it might happen...
*In Nostalgia Critic mode* So let me get this straight... the movie's about Jason Segel who wants to hook up with Amy Adams Whose Still Being A Redhead Right Now Which Makes Her Look Like Jenna Fischer, and he's thrown the Muppets in there somewhere, but that's not important... ?