They're both "Protect Game" brand, and their internal layout is identical on both case types. My guess is that the black cases are an older model, and the company behind "Protect Game" made the newer versions slimmer at the request of rentals. A slimmer case, after all, means that you can fit more on the shelf, and also the slim ones are much easier to print up inserts for (as I discovered) since they fit on standard 8.5 x 11 paper. Also, the clear cases may have been preferable to some renters for security reasons.
Basically, my guess is that the black cases are older, which makes them "1.0," wherase the clear ones are "2.0." The older cases aren't bad in terms of their construction. The black plastic looks cool, and the thicker spine reminds me almost of a mini version of the "shock boxes" that people use for Neo Geo games. However, they're certainly not very convinient if your goal is consistent casing that's easy to print inserts for, which is why I opted to pick up more clear cases. I don't plan on returning the black cases since they may be handy in the future if I pick up any non-Sega or Nintendo retro systems, but for my Nintendo games, I'd prefer to stick with the clear UGCs, and for Sega Genesis / MD, I'd prefer to stick with the official ones (of which I have plenty).
