FWIW I may have seen this before myself when trying to change sound files. Think of it like this- chain files is the operating firmware and as such a function points to a memory address. The idea is the sound file matches that address. However, if say they changed that scheme of what sound file memory location to a given function call, or as features were added and sound functions added it was different, then you could get the exact problem- a function calls an invalid memory location and you get bad noise.
So yes, I would use matching chain and sound files.
Now catch22. I know that there was the EMI compliant boards VS non-compliant EMI boards, and that newer chain files are backwards compatible, but old chain files on an EMI-compliant board is to be avoided. EDIT per John, Very bad things can happen on a steam boiler board that is EMI-Compliant version (newer) and putting old chain files from a non-compliant era board based engine.