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I believe that I've added more debugging code than actually fixing problems.
But hey. Maybe I still need it later on if something goes wrong again.
The problem with the strange "Value must be positive message" was fixed.
MOD samples are generated using 16 Bit BASS samples instead of 8 Bit. This fixes this strange periodic noise which was generated before.
Also the original frequency of the sample is ignored as target frequency as for ProTracker only certain base frequencies can be used.
I hope this is satisfying to you. I haven't programmed C# for about 10 years and my experiences with MOD files might be not as much as you have.
Tested with:
mono Xrns2XModShell.exe resources/examples/test_mod_sample_conversion.xrns -t mod --out test.mod