Using Neto Bootloader which fixes the infamous sound issues that AtGames systems were plagued with, I loaded up the patched ROM on my AtGames portable, played the game some, bribed Knuckles, and then...nothing. The game had crashed! You can see it in action here: https://youtu.be/minMwpBwInA
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No dice. The built-in SD loader exhibits the same behavior regarding the special stages. Additionally, this even happens in original mode, despite the original game behaving without a hitch.
The original is one of the built-in games on that thing, and they at least had the decency to make sure it works (surprising considering the aforementioned sound issues). That said, I haven't thought to test DX using the built-in SD loader instead of the unofficial Neto one that fixes the sound. I'll get back to you on whether that makes a difference.
I am not sure if this can be considered a bug with the game. You are using an AtGames system, yes? From what little information I have regarding that, the hardware is either mimicking actual Genesis hardware or acting as an emulator. In either case, if something is going wrong on this system which is not occurring on an actual Sega Genesis or an accurate emulator like Kega Fusion or SEGA Genesis Classics, then it is a fault of the medium in which you are playing the game, the AtGames system. Perhaps if you check that the original game works fine, it can help to diagnose some game-breaking special-stage bugs?