I wonder if that's because you used a cable based on the FTDI chipset instead of the Silicon chipset that the YPS was written to use.
In any case, the explanations in the manual for the YPS might help you to understand what you're seeing in Chirp.
If there's a way to inhibit transmission on specific channels after you deliberately open up the frequencies, I don't know what it is. I haven't looked for it either. Presumably some of the bands are receive only.