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I'm guessing maybe it just needs to be rebuilt. There is a file called PADDING.DAT, that I thinking is the dummy file?
I tried upgrading my firmware, and when I do, my PS2 doesn't recognize my non-sony 16mb memory card (which holds Infinity Manager and my HDLoader). But I did try the burned MC3 with the updated firmware, and it didn't work. So I'm guessing it's the burn.
Would PADDING.DAT be a dummy file that I could get rid of?