I have an SB Audigy 2 zs and I HAD the same problem. After some days of testing, I traced the problem down to the scene.dat file (I was trying some of the early scene.dat mods at the time). After I switched that scene.dat file for another scene.dat file the snaps and pops stopped, so it may be a file like that which is causing you problems.
If you have the basic SH3 with 1.4b, try lowering your audio hardware accelorator under the contol panel.
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