Here's what happened.

The Rhino versions were remastered from the original 35mm negatives. The negatives were the versions originally sent to the U.S. from Japan, and sometimes there would be scenes with animation errors, coloring errors, or things which the American directors judged to need improvement. They would then order "retakes" of those scenes to fix the errors. However, these retakes were on separate pieces of film, and some of them were never edited into the master negatives. The retakes were instead cut into the episode after the film was transferred to videotape.

Rhino went back to the negatives for better image quality than the 1980s video masters, and consequently reintroduced errors and rejected takes. Sometimes, they tried to fix coloring errors by digitally repainting them, or did other digital tricks. Unfortunately, being done at SD resolution, they looked like crud and didn't really improve anything. Sometimes, they changed things that were on the final aired versions.

Eventually, Rhino's license expired, and a few years later, Hasbro re-licensed the Sunbow cartoons to Shout! Factory. For Transformers, they dug up the original broadcast masters to reinstate most of the retakes, but according to that site, it seems they just for G.I. Joe they just reused the Rhino remasters and synched them up with the original mono soundtracks.

Here's that site's review of Shout's Transformers season 1 DVD set, maybe it'll be more concise than my version: http://www.cartoonreviewsite.com/eds/ed7.html

I hope I explained it well enough; anybody else, feel free to add anything.