mednaffe
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"syscard3.pce" expected checksum is incorrect
The MD5 of the correct "syscard3.pce" file is (from HERE): 38179df8f4ac870017db21ebcbf53114 which has SHA-256 value: E11527B3B96CE112A037138988CA72FD117A6B0779C2480D9E03EAEBECE3D9CE
the expected value in Mednaffe is different.
Yes, it seems that syscard3.pce file from Mednaffe has padding zeros at beginning so I'm afraid you're right.
I don't know why I jumped to the conclusion that it was correct. Let's me ask about this on IRC.
Thanks for reporting this and sorry for late reply!