often a fouled plugin can cause pops
not sure these are the ones you are experiencing
they have occured when moving channels around or when stopping play back
a quick little pop sometimes running through effects, verbs etc
you can usually fix by reinserting the plug in
if you want to preserve the setting
try clicking on it with both control and apple down
that will uninstantiate the plug
then do it again to re instantiate
the often cures it without having to reinsert and lose the settings
i hope this is it and it is this easy to help you