Disney also owns Marvel as well, and wasn't the Muppet Babies co produced by Marvel?
Television production companies rarely matter when it comes to animated adaptions. Usually the copyright for the show goes with the copyright holders. I'm not sure if it's correct, but that's usually because said copyright holders are the ones that fund the cartoon series. CBS released Filmation's Star Trek while WB owns Filmation's DC cartoons, The Real Ghostbusters, produced by DIC, is owned by Sony, and Henson owns the Fraggle Rock cartoon, also produced by Marvel. There are some cases where the animation production company retains rights to the show (some of Dic's works, but that's because some cases the copyright holders couldn't care less... like the Nintendo cartoons), or shares copyright (like in the case of He-Man... Mattel co-owns the characters with Entertainment Rights, especially the toy rights).
Then there's the messed up case of Saturday Morning Supercade. Every segment is owned by a separate company, and will likely NEVER be released on DVD, even though Sony has official online episodes of Q*bert (as they own the character). Yet Warner Bros has the rights to the other Ruby Spears video game cartoons made in the 80's, Pac-Man and Dragon's Lair.