Agreed - there's issues with the cast (which is insanely large, mind you) receiving royalties from broadcast/distribution of the show.
Nickelodeon doesn't own the show, CJOH in Ottawa does.
Nick had a contract with CJOH up until 1994 allowing them to show reruns of You Can't Do That on Television as they pleased. Once the contract expired, Nickelodeon stopped airing the show because they would have had to pay royalties depending on what episode they aired, and to each individual cast member featured in that episode.
So when Nickelodeon had their 20th anniversary in 1999, they bought 5 episodes outright from CJOH to use without having to pay royalties. They aired 2 or 3 of those episodes during a marathon.
Then when Nickelodeon had their 25th anniversary in 2004, the two episodes they ran were Pop Music and Enemies and Paranoia - which both aired during the 1999 marathon.