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Attachment contains my FTM and two NSFs. One of them was built with the newest Famitracker, the other was built with an older version. The one built with the newest version is completely hosed.
There are a lot of things that don't seem to make the transition between FTM and NSF... I had a few rants in the IRC channel but now I don't remember the specifics.
I'm just going over it all, it sounds like the volumes are being translated over, but it could be the the arpeggio causing the problems.
Dwedit, instead of making all those new instruments for all the duty cycles, and utilizing all those arpeggios in the instrumentation, have you tried utilizing the Vxx (pulse width change) and/or the 0xy (Arpeggio) commands in the pattern to see if the problem still persists? (or maybe you can try a new pattern near the end of the song and do some "tests" to see if it fixes it)