I have gotten that sound as well. I've got a 5/99 production X that is a 4x2 auto SE. I've noticed it when I have to break hard and after the truck has rested a minute or so it will "clunk". Sometimes happens when I start to come off the brake. I haven't found it to happen that frequently and haven't really worried about it.

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LadyVolFan
2000 Silver Ice 4x2 SE
SouthEast Xterra Club