My Titan does the same thing. First time I heard the noise it freaked me out a little. It doesn't always make the clunking sound; just periodically & the AC cools nicely. My Z3 does the same thing only it isn't quite as loud. I've also noticed the compressor in my '72 Monte Carlo makes a loud clicking sound as does my bud's '69 Camaro. I guess they all have their own quirks!
If it keeps up Phoebisis and you want peace of mind, take it in and let the dealer check it out. Keep us posted.

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Rick
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2004 Titan King Cab LE 4x2
Canteen Green
Graphite/Titanium Leather
Splash Guards
Floor Mats
Hood Protector
K&N Air Filter
Wood Dash Kit
Chrome Trim on [black] tailgate panel
Built Jan 2004; Purchased Feb 29, 2004