Disney is generally bad with not getting all the seasons out for their shows (IIRC, a lot of their animated 90's fare also has the problem of eternally unannoucned later seasons). Clearances are probably not the problem- they'd just cut those scenes out of the episode like they did for other Muppet video releases.
Just watch The Muppet Movie for the first time last night. What great, (almost) clean fun it is. I say almost because of... well, it got the biggest laugh out of me, but Mel Brooks licking the torture machine is more than a little odd. On the whole... the Muppets cinematic ventures seem to be fairly solid. I haven't seen Caper, or From Space, but TBH, there are worse film franchises out there.
@jp-30 made me think of you... http://www.threadless.com/product/3375/The_Circle_of_Laffs/tab,guys/style,shirt
That one has me stumped... not sure who that's supposed to be (I'm guessing Beaker). Ralph should be in that spot, though.
Er... well, the background color for that space could be changed. So yeah, anyway... it's a pretty awesome t-shirt. I wouldn't mind owning it.