On the lack of Kermit...
I checked on this issue and the lack of Kermit is not Henson's fault. It's Disney's! Back when Henson produced the giant Emmet Otter "Collector's Edition" DVD back in 2005 they tried and tried to get Kermit. Craig Shemin (who produced the set and the awesome new bonus features) fought long and hard for Kermit - as did the Jim Henson Legacy and Henson Company. But Disney said no. Henson and HIT made every effort back in '05 to get Kermit for the "Collector's Edition" (even if that meant paying Disney for the frog's scenes), however, Disney would not allow it. I checked with some friends at Disney and they backed this story up. Disney's policy is they don't "rent" the rights of their characters out to the competition (Sesame Workshop, which is a non-profit, has a special deal with Disney -- and other guest appearances have other pre-arranged stipulations). It's sad, but Disney is the "bad guy" in this situation - not Henson/HIT/Lionsgate.
I know that you checked on this back in 2005, but did you check again recently when The Christmas Toy was released? Because I wonder if Henson even bothered this time around to try to get permission to show Kermit's scenes.
When you mention the gues tappearances stipulations, are you referring to pre-2004 guest appearances, post-2004, or both? Interestingly, it seems that Henson is the only company that's been a victim to this, having to cut Kermit out of Emmet Otter and Christmas Toy. I don't know if other companies have had troubel releasing DVDs with known Muppet characters. I recall that the Nancy Sinatra special with Muppets was going to be released some time ago, but plans were cancled. I wonder if it was because of the use of Muppet characters.
But still, since Disney bought the Muppets, some of the Muppets past guest appearances have been released on DVD, including the Muppets on The Cosby Show and some of Rowlf's appearances on The Jimmy Dean Show. Disney may have a policy of not licensing it's characters to the competition, but I think that in the case of the Muppets (or any other characters that Disney didn't originalyl own rights to) in outside productions Disney should make an exception. Judging by the interview with Lylle Brierr (or whatever the name is) on The MuppetCast it's obvious that Disney (or at least the Muppets Studio) really care about the Muppets and the fans. Still, Muppets Studio may or may not have controll over some things.
I recall that long before Emmet Otter was released, Dog City was released by Hit! in the UK, with Rowlf's scenes included. Have you thought about doing any research to see how this was possible?
And I wonder, does Disney see Henson as a rival?