Are you using cheats when testing the level?
If so, remove them. They cause Red ?-Blocks to not appear sometimes.

I have this problem too. Sometimes, when the redblock is on the worldmap in the level I enter, the hammerbro appears instead, despite I did put the ? red block sprite in the game. On the worlds that dont have a hammerbro, the ? red block doesnt appear at all. I wonder whats wrong.
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For me that problem only happens, when I unlock levels with ar-codes.
Red ?-Blocks and Hammer Bros are bugged then.

I havent used any AR codes. I think it has something to do with an unknown level header flag. Since I am having problems with the area midway entrance I want to appear, since I have imported into all areas a level that has settings as a priority level.
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I will try someday to look onto it. might be some undiscovered level headers settings. I wonder, on the level you are having problems, have you imported other levels onto its areas?
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That may be the problem, but I dont know why would AR codes mess up the flying red ? block.

Ill ask again, have you imported on the level areas you have trouble, other levels?
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Well that may be. I am using a completed .SAV  ray provided a long time ago. Ill test with a new file, but testing this is not that easy, since the flying red ? block position randomizes...
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Codes defiantly mess up ? block and hammer bro positioning.