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It will be due to the true bypass switch I believe a resister can be wired in to reduce the pop but I'm not to sure.

If it is relay based like Mystic says, then the same kind of problem can occur as with conventional true bypass pedals. The specifics of the issue are kind of unimportant, but if you want to find out you need to look for posts about leaky capacitors and DC offsets, that kind of thing.
Yes, a resistor wired in the right spot can help, but it never solves the problem entirely. You'll probably also find that if you change the order of your effects that the click will change or disappear entirely.
I'm yet to find anyone who's come up with the silver bullet solution. The best way (IMO), if you know how, is to change the output capacitor (which is likely electrolytic) for a low-leakage variety like a mylar film or polyester capacitor.
I don't think the GT2 is true bypass - I'm almost 100% sure it's like every other SansAmp pedal, with a relay-based switching setup.
Anyhow... there really isn't much you can do about the popping. It's a consequence of some types of switching systems.
Usually, you only see that problem with true bypass pedals, and it's random. Example: My Little Big Muff sometimes "popped" when switched on and off, but my Clone Theory never does (and the switching is identical). Not all Little Big Muff pedals will pop, and some Clone Theory pedals will.
I've never heard of it with a GT2; the switching system they use on it is supposed to prevent that sort of thing.
I don't think it can really be modified, either; it's a pretty dense circuit. I'm guessing the switch is old or worn out?
some gravedigging here...
as i understand this, you just have bad luck when this happens?
the clicking i have (hartke bass attack 2) only occurs when a note is ringing, if the bass is quiet theres nothing (thats probably normal, dont know...newb and so)
Clicking while it's already on...