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I know about Famitracker since a year and downloaded it back then, but I actually started composing music with it since one week. And I ran into my first problem:
When I want to play a chord, let's say A-2 and A-3, there happens a phase cancellation and I get an inconstant sound. I've been testing some NSF from commercial games and I still can't get it right.
There's an example of the problem. It's track number 2.
In this demo I have chosen the second pulse channel as a 25% pulse instead as a square one. This was the original setup, the other one I posted was testing if I can bypass/reduce phase cancellation by using a square. Also I turned up the volume of the second channel a bit in order to make the problem better to hear.
Edit: I guess the only way to achieve good harmonics is making the volume lower, which is not that great since the outcome won't sound as aggressive as I wanted.
I got that you mean, though your example barely demonstrate the problem. Seems it's problem with FamiTracker sound code itself, because NSF in external player don't have that problem.
[url=http://shiru.untergrund.net/temp/pulse.ftm]Here is my demo of the problem (shows unstable pulse beat in FamiTracker, not audible in external players).
You can try a quick-fix which may or may not solve your problem, add a fine pitch change effect to change the phase correlation and hopefully make the two wave forms play nicer with each other. If anything you'll get a cool little phasing effect which should help increase the punchy sound you're trying to achieve. So, try adding "P84" to the note on the second channel and see if that gives a more desired effect.