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Professor Hyde White is hidden in a wooden Indian in the comic.
In the comic, Velma brings the clue of the special magnifying lenses back up.
In the comic version, however, Scooby simply...trips him by accident.
In the show, the Black Knight chases the gang around the museum in a lengthy, gag-filled sequence. Not so in the comic.
In the show, Shaggy and Scooby are the ones confused by Fred's declaring that the mystery is solved. In the comic, Velma is just as surprised as Shaggy, perhaps because they're just now rejoining Fred and Daphne.
In the show, Fred and Velma solve the mystery once Daphne points out the duplicate paintings. In the comic, Fred solves the mystery by himself.