Random (and annoying) Clicking Noise

First post. So, bear with me.
I'm semi-new to GarageBand, been using it for a bit now. I recently recorded a full song, drum track, 2 guitars, bass, vocals. I mixed it, mastered it, etc. That was all good and dandy.
I have, however, now wanted to go back and play around with it.
Yet, everytime i open the file, there is an incessent clicking noise. Sometimes it is on specific tracks and if I mute those, it goes away, but sometimes it permeates the whole song.
Does anyone know anything about this?
Oh, the clicking sound IS effected by any applied FX, and also happens on tracks which have no recorded media in them yet.
MacPro   Mac OS X (10.4.8)  

You said it wasn't the metronome - have you turned it off?
If you record a vocal with monitor ON but plug headphones into the Mac's headphone socket do you get the problem.
Are you getting overpeak warnings on GB's meters - track or main?
If you import a recording (one you know to be OK) from elsewhere into GB do you get the problem? (If you want one to try: http://www.macjams.com/song/28234 and click 'download' - probably not your sort of music but I can promise you it has no clicks, though it does have a fairly heavy bass drum.)
If you play songs in iTunes do you get the same problem?
If you reduce the master level in GarageBand does the problem stop?
How are you listening - the Mac's internal speakers, speakers connected to the headphone jack...?
If you turn down the Mac's output volume and/or any external powered speakers does the problem stop?

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