I have a sort-of similar problem - I use Tone to make a little warble, sort of sounds like a cell phone ring.
Imagine dee-dle-dee-dle-dee-dle-dee-dle-deeee - and this afwul farty kind of noise as it turns off. I have 5 boxes - 4 smaller, 1 larger. All the same circuit, output pin driving a mosfet then the speaker. Only the larger box makes the noise. Nothing I've tried stops it. And nice & loud too as the MOSFET switches ~ 3W across the speaker (12V source thru a 34 ohm resistor into capacitor coupled 4 ohm speaker).
We just laugh about it now, especially when people hear it.