My pedal pops!
"My pedal pops when I step on the bypass switch. What's wrong?"
It's a true bypass (TB) pedal, isn't it? If so, it's an interaction between the TB circuit and one of the surrounding pedals or the amp.
Popping is a well-known problem with TB pedals. It comes from a small DC level shift as the bypass switch disconnects one set of circuitry and connects another. The leakage current through a coupling capacitor (or from the grid of the first tube in your amp) develops a small voltage across whatever resistance is present at the inputs and outputs of the connected device. The leaky capacitor can be in one of your other pedals, in an active pickup or preamp in your guitar, or even in the TB pedal itself.
Some players find that toggling their TB stomp switches a few times before playing helps to reduce the severity of the problem. The theory here is that there's more time to build up a charge between the time you set up your rig and the time you start playing. Once you're playing, the stomp switches change more often (therefore less charge buildup and less popping). Plus, it's harder to hear the popping over the "roar floor" of the band. The downside of preemptive toggling is that those 3PDT switches have a finite life expectancy; they're not exactly cheap to replace.
Feel free to ignore the following soapboax diatribe, especially if you really like true bypass...
On the surface, true bypass seems like such a good idea: don't run the uneffected signal through any necessary active circuitry. There's nothing but "pure" metal-to-metal contact all the way through the signal chain. The problem is: there are drawbacks.
The popping is one such drawback.
Another drawback is the variable loading on your guitar's pickups as you engage effects closer (along the chain) to your guitar.
Another drawback is that the 3PDT switches are prone to failure.
Finally, those connectors and switches add capacitance to the signal path, which lowers the resonant frequency of your pickups and reduces "sparkle", often much more so than a few good buffers stacked up would do.
Of course, you can eliminate the capacitive-loading problems by putting a buffer at the head of the FX chain. (Or you could put the buffer after any FX that don't play well with buffers, like fuzz and some wahs.) But then you have a buffer in the chain. Weren't you trying to avoid buffers by using true bypass pedals?
And-oh-by-the-way: the added buffer doesn't solve the popping problem.
The FET-based "silent switches" (used by Boss, DOD and other pedal designers since the `70s) are the right solution, IMO. Yes, there may have been some cheesy buffers in some of those pedals, but that's an implementation detail. You can always throw more money at the problem to build a better buffer. (The buffers in the Visual Sound pedals, for example, are quite euphonic.) You can't make the true bypass popping disappear entirely and still have the purported benefits of true bypass. (The so-called "solution" to the popping problem is to resistively load the inputs and outputs of all of your true bypass FX boxes. These resistors load down the guitar pickups, which reduces their sparkle. Back to square one...)
When small builders found "gold in them thar hills" by cloning classic designs using "designer" components, they ignored the silent switching system, partly because the switching system itself tends to be more difficult to implement than many FX circuits and partly because - if you ignore the system-level aspects of the solution - true bypass switching seems like a good idea.
Rather than putting in any real R&D effort (better silent switching systems; better buffers), it was easier for small builders to finesse (i.e. ignore) the problem by using a 3PDT switch in a true bypass circuit. Follow that up with some good old American marketing to turn a weakness into a sales pitch, and voila! The cult of true bypass was born...