Many .NSF files available online fail to include the initialization of the SOFTCLK ($4017) register, potentially causing triangle channel notes to be played incorrectly, among other subtle problems.
I noticed this while creating a pack of Wizards & Warriors, where this makes quite an audible difference. When creating a pack from a .NSF file, be sure to always check whether the game writes something to $4017, and if it does, check whether the .NSF from that game does as well, and if not, then add that instruction to the .NSF file yourself, or look for a "fixed" version of that .NSF, for example on
this website.
I have not checked how many existing packs are affected, but if they are, it should be possible to fix them by just adding the appropriate write to the beginning of each .VGM file.