Okay, the problem is far easier than that.
Given the path in your screenshots, I suppose you wrote a python script to extract the MO3 files from the game's data file. However, you didn't open the input and/or output file in binary mode, which typically means that on a Windows systems, the characters \r and \n are automatically converted into a Windows line ending (\r\n). As a result, the file you extracted differs from the original data file. To avoid this conversion, binary files must always be opened in binary mode, not text mode!
If you follow this advice, you can extract the music correctly.