First a note: Higher value pulldowns
increase the likelihood of popping. You could try temporarily decreasing the value of the pulldowns. That might affect the tone, but will let you know if that's where the problem is, though this is very unlikely to be the case.
Other possibilities:
-
Led popping: try disconnecting the led to see if it still pops.
- A bad switch: try a new one, or try manual switching with a breadboard or roach clips or something
- A solder bridge somewhere