I feel a bit foolish because I wrote Henson a letter requesting they put the songs back where they belong (due to info I got from fans here.) Turns out that the two songs were never in the theatrical version- whether they shot footage for the songs and then edited it out (then they SHOULD release them,) or just decided not to use the songs before they filmed the movie like "Dr. Tooth" mentioned (more likely,) nothing is missing on the dvd from the theatrical release (Oh, except for a big chunk of scenery and action on each side of your tv.) The songs were included on the CD soundtrack though. The soundtrack sells for a lot of money around this time of year on Ebay, but I saw copies of it last year at Duane Reade in NYC for 7.99.
And I think it has been confirmed that the "Muppet Family Christmas" DVD is not missing anything that the VHS version from 1992 has. I did not buy the DVD last year because I thought they hacked it up even more, but turns out that it's a case of 5 advertising minutes that caused confusion. Go out and buy Muppet Family Christmas- if you haven't seen it, I think it's one of the best Muppet products. I'm going to try not to compare "Very Merry Muppet Christmas Movie" but I'm anxious to see if they can get a piece of the magic that MFC had.