I think that sounds pretty much normal for Live - all these clicks and pops and glitches are one of the reasons I've recently switched to just using hardware now - they did my head in. I used a Delta 1010 soundcard and spent months tweaking it to within an inch of it's life, didn't really help much.

Like the previous post said, check which version you're using and update if you can. The only other thing I can suggest is to actually cut out the section you want to use, apply the effect (maybe in a wave editor eg wavelab) then just trigger it as a clip whenever you want.

Should free up some cpu cycles and avoid the dreaded click...