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It's because you are using two squares in unison; if they're playing the same frequency they can end up cancelling each other out.
I recommend not doing this. Either just get rid of the redundant channel, or put a detune on it, like P7F or different vibrato settings from the other channel.
Ah, OK. I should try the P7F approach I think, because I like the sound that 2 redundant square channel gives in this tune. There's not much going on in the song, so the square channel needs to be strong. Does anyone else agree? I'd like to make this one as good as possible! I'm sure I have the timing and notes down, the main things i need help with is vibrato and tone, I think.
The thing about redundant squares is the tone you get will not be consistent. They can be in phase, which will be twice as loud, they can be out of phase, which will be silent, and they can be somewhere in between, which has a variety of tones.
Which of these you get may be predictable or random depending on a lot of factors, choice of emulator particularly, but it's generally very hard to rely on it.