Both the Sonic Turbo and the Pitch Black have a few users who report this 'pop' issue, and from my experience it has at least something to do with what else is in the signal chain. My Turbo Tuner is totally quiet when switched, but a few get pops when bypassing. I had this problem with the active/passive switch on a Pope preamp. It only happened with my Thunderfunk amp. No other bass had a problem with the TF, and the Pope didn't pop with any other amp. Dave put some sort of capacitor somewhere in the input stage of the amp and it never was a problem again.
Yeah, all but one of my pedals are true bypass and I have a couple that pop. It seems to be more related to the pedal itself than the chain though. One of them, a mosfet boost pedal that I built, was popping when I engaged the pedal - due to the LED. The only way I could get it to switch silently was to power the LED from it's own battery (I just wired 3 watch batteries together). Here and there I've borrowed a TU2 to tune up on gigs and in the studio and it was on my list for a long time. However I never felt comfortable putting it in my chain because I've had such bad experiences with Boss pedals coloring my sound when bypassed - thus the obsession with true bypass and my delight with the Pitch Black.
Ralf