First off, This is my first post. Glad to be part of the forums.
Second, This is a spoiler related bug. If you have not beaten the game yet, turn back now.
After I caught wind that there was an alternate path on the final boss, the police escape, by setting the render method to software, I immediately gave it a shot, had my fun, and set it back to OpenGL. When I decided to go for a replay on the original final boss (Shark robot), the game still set me through the software mode final boss despite checking that I was still set to OpenGL. The shark robot was even in 3D and everything. I'm not sure if this is a bug or you can only fight the shark robot once. Are there any workarounds until this gets patched?
If you look at the blue door on your right when you go to fight Protoman, it'll trigger the Software final boss. This is only accessible after you defeat the Shark.