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Gunvor Nazarian
We spent about 3 weeks trying to figure out why dispyz's datarunner .mod wasn't working for use in the tracker hero game. I remember him writing it on octamed soundstudio and throwing a rage when neither winamp or renoise would play the sound file. I asked if it worked in protracker, and when it didn't we knew something was up. I'm sure there's an easy answer but Amiga tracking and beer usually go hand-in-hand.
Anyway, I wish I had documented some of the process, but I do remember having to go into protracker and adjusting various settings which seemed to adhere to the incredibly strict rules of the .mod format. Octamed was certainly a little more lenient and opened files as .mod when others wouldn't.
About the sample noises, do they appear at the beginning of samples? If so, perhaps they are some sort of header (non-raw sample format) or other meta-data, so you should double-check anything you did with the instruments. Smartest thing would be to start a new module in milky form scratch and keep fiddling with it until you manage to make it not load in protracker. Using an emu would be simplest for this.
Frankly, whatever this is, it should be treated as a bug and reported. Milky is supposed to let you know if you did anything to break the mod compatibility.
I'll try to load all my milky-modules into protracker, see if it's a common problem.