I don't know the exact reason why this special rarely airs, but I do know the PBS likes to keep its programming current and up-to-date. So a show featuring the BSBs really puts the late 90s/early 00s date on it. (Maybe 9Story could do a remake with One Direction or something. I'm sure Muffy has a crush on one of those boys, too.
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As previously stated by Earwig, this special is kind of hard to schedule. It IS an hour long, which means that it takes up double the time of a normal Arthur timeslot. On top of that, there is not a certain time of year when this special is particularly appropriate. With the BSB thing on top of all that, it very rarely gets scheduled.