1) There is something strange going on: on my system I can process a file size of 5.094.600.192 bytes without any problems (though the progress bar does not progress correctly

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I'll first have to find a way to reproduce your problem before I can mend it!
All the same I will try to get the progress bar to behave correctly.
2) The only thing the Joliet checkbox does is replace the ";" characters in filenames as they appear in the MD5 file by "_" characters, as Nero doesn't like semi-colons when the ISO 9660 is used. I find this setting highly useful and I always have this box checked. I will see whether I can change it so that MD5Maker remembers this setting.