Again: all I know is what it says onscreen. I'm not an expert, I'm just looking at the pictures and extrapolating. I didn't see an onscreen Paramount copyright on TAS, although they do have a copyright on the novelizations.
The episodes do end with the Paramount logo, although you're right, the copyright doesn't list the studio, just Norway and Filmation.
That was around the time he died, wasn't it? So maybe the family, or Roddenberry's lawyer, sold the rights then.
The budget is dated April 12, 1991, about six months before Roddenberry's death. It's possible the estate sold the rights to Paramount at that point, but if they were getting a million dollar license fee per movie, I don't know why they would.
I thought the court rulings from the mid-1990s between Roddenberry's estate and his first wife might shed some light on the issue, but there's a lot of information to go through there. From skimming the documents, it's possible that a 1986 contract between Roddenberry and Paramount transferred some rights to the studio, but I'm no legal expert.
But, I think we've derailed this thread far enough at this point. Back to the original topic.