Hmm. I get this in logic when I'm simply running too much through it. I have a dual 867mhz G4 and I push about 46 exs24 VSL instruments through it ... also running reverb and stuff... so yeah the initial playback is none exsitent .. have to keep pushing play and when it stops giving the "Could not processor audio in time" error ... push play again.
Until finally it behaves and pplays properly. However when I try to record melodies on certain instruments the sound is totally broken up, but the signal is recorded okay .,. and usually on playback it's okay.
So what I'm saying is that for me this crackling problem occurs cos of the amount of processing I'm asking my poor little mac to do. Your G5 really should be able to handle this. So I'd say have a good look at your ram .. perhaps it is defective .. even perhaps the problem could lie with your second processor (though there'd be other problems with your mac if that were the case).
Best idea .. though it's a pain in the ass .. reinstall Mac OS and everything, though you might wish to take out the ram modules and see if the crackling occurs with certain ones running in the machine.