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Yeah, I'v noticed the same thing on my '08. The manual trans is actually a little noisy. One of these days I'll change to a differant fluid and see if that helps.
Mine was really noisy about 5,000 miles after I first got it. You could hear the synchros whining on decel. I took it back in and had them replace the synchros under warranty. Fixed everything. The cluncking is normal though.