Okay, so zero is a valid number in this assignment:
frequency = reference * 2 ^ (1/12) ^ 0
 
In that, 2 ^ (1/12) ^ 0 = 1, so a scalemapping of zero translates to the reference frequency: reference over one, which, if your reference frequency is 440Hz, 220Hz, 110Hz, or 55Hz, is a 12-TET Ay.
 
FracTint will use zeros if you enter them manually. It will also save them. I won't load them from parameter files. It should not be treated as it is, though, because that means two Ays are possible in a scalemapping: Zero and Twelve.
 
I've been using zero to reprezent silence for over ten years. That's what M$ QBASIC does. It was a bit tricky to get a neat zero in my synthesizer, when I decided that the PC speaker didn't offer quite enough in the way of parallel harmonics and neat sine waves.
 
If I want to change it, I guess the easiest way is to read the code myself, splice in a special case for zero, where all of the Cs, one of which would normally be at about 65.4Hz, become silent: compile it in, and offer it on the developers mailing list when it works.
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http://ecn.ab.ca/~brewhaha/Sound/