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In the comic, Fred and Daphne are alone when they discover the paint clue...
In the show, the gang is quickly reunited. Shaggy notices there's a picture moving, but when he brings the rest of the gang over to see, it's already been replaced. None of that happens in the comic.
In the show, Scooby hides in a planter. In the comic, he hides in what appears to be some kind of ancient covered vase.
Velma mistakes the Black Knight's angry groans for Shaggy's cough. Luckily, she happened to be carrying his medicine and pours out a dose just as Shaggy rushes by. They run off, apparently oblivious to the Black Knight. (In an animation goof, Velma's wearing her glasses again.)
In the show, Scooby notices the Black Knight and knocks over Velma as he runs away, causing her to lose her glasses. The Black Knight trips over Velma and falls into a stockade.
Velma doesn't tie up Scooby's muzzle to keep his teeth from chattering in the comic.
The comic cuts the part where Velma and Scooby get separated from Shaggy.