Recently when recording I've started having trouble with clicks and pops while recording bass. Its DI'ed going through a V-amp Pro (essentially bypassed settings wise) through into my Delta 1010. Strangely in only starts to occur after a while -usually a few minutes - and only in Reaper. The problem doesn't occur when sending the signal directly to the monitors from the sound card.
https://dl.dropbox.com/u/7153764/crackel.ogg
This wee audio clip shows the problem. The first half is while using Amplitube 2, the second without any effects. I haven't yet played around with many settings in Reaper but I honestly don't know where to start or what it could be causing it.