I’m glad to hear you are liking the Quaverato, but I am sorry about this issue.
It sounds like you may have some leaky optocouplers. It seems like light is somehow making its way into the heat shrink, causing the signal not to shut off all the way. Please make sure you seal the ends very well with some opaque substance (even poster putty/sticky tack will work). Also, make sure you optically seal the holes you made in the heat shrink.
You can use calibration mode to tell what side (high or low) is leaky. Also, it’s best to use the square wave setting with the depth all the way to 100% (fully clockwise) and the LFO rate set relatively slow, so you can easily hear if the sound is not shutting all the way off on each cycle.
Good luck!
-Brach