I posted this in effects too and thought you guys might experience this too. So I have a few pedals (ok ten). I use them quite a bit during songs switching on and off during bridges, guitar leads, ect... I play at church twice a week and most of it is new Christian Contemporary music. I have invested more money into buying only high quality pedals and cables to keep the hiss and buzz down because in worship/church the sound team frown on ANY noise. The last couple of weeks the sound department has been complaining to me about clicking on and off my pedals and making that true bypass click sound. The funny part is the guitar player has around 16 pedals with clicks and OD buzz and he never has been told anything. Does anyone else get complaints about there pedal clicks?
If noise sneaks in it can be emphasized with the pedals clicking in and out of the chain. You might need a gate, and only switch when you're not playing. "True bypass" is kind of a gimmick. Keeping the levels and loading the same before and after the pedal clicks in is what you want. You need some buffering when the pedal "effect" part is bypassed.
True bypass pedals that pop (electronic, not mechanical switch noise) need pull down resistors on the inputs and outputs, to keep caps in the pedal discharged. When an input or output cap is connected to the live line when the pedal is switched on, it will pop. A pulldown resistor keeps this from happening or minimizes it. If the click is the mechanical click from the switch itself, then replacement with a quieter switch is needed, or a bypass strip with quieter switches. They may be running a compressor/limiter on the bass channel that is making pops louder in the PA than you hear in your rig.