+1 on the chain pin as a possibility. When I was building up my LaRaza, I bought a Shimano Ultegra chain from the LBS, which they graciously measured to proper length and installed. The hotshot tech didn't take the time to find the proper Shimano pin tool for the thin chain, so the pin didn't properly seat in the far sideplate. After putting about 100 miles on the chain, I noticed a clicking sound that didn't correlate to equal pedal rotations and was going crazy trying to identify it. It also started shifting by itself under any type of pedaling effort. When I finally found the problem, the side plate had already separated from the pin and was on the verge of coming completely apart. The LBS made good on a new chain, installed by a different tech with the proper tools under my watchful eye....
B'Dog
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2006 Gary Fisher Marlin MTB
2004 Salsa LaRaza aka "Mmmm, Blue Salsa" (853 steel is real, baby!)
2003 Kona Humu Humu Nuka Nuka Apua'A Singlespeed - Gone, but not forgotten
1998 Diamondback Outlook MTB
1990 Centurion Cavaletto 'Gaspipe Beater' Roadie
1978 Volkscycle 'Frankenbike' CroMo Tourer