Well, the characters from SST ARE still Muppets after all, so really, there is not misidentification when it comes to "confusing" them with the Muppets.
But anyway, to clarify what Drtooth has said, when Jim was originally dealing with Michael Eisner over the deal of the Muppets, Eisner did want the SST Muppets included in the deal, but Jim said no, that the deal was to including only what we now refer to as the "Classic Muppets" (Kermit, Fozzie, Piggy, Gonzo, etc)... then no sooner did Jim die, then Eisner basically tried to steal the SST Muppets away from CTW and JHC, thoug luckily, they fought back over that.
Personally, I don't want Disney to own the SST Muppets, frankly, I don't want any more of Jim's empire sold off... my respect for Brian and Cheryl and the rest of the JHC is already at an all-time low, what with them selling out the Classic Muppets to EM.TV then back to Disney, then just giving away the rights to Fraggle Rock, etc.