A chain should last many thousand miles, but if it has not been maintained properly or if it's simply defective, it can get tight links that cause it to intermittently get tight on the sprockets. "Appears to be clean" is actually probably not a good thing, since a properly lubricated chain usually looks a bit greasy and dirty.
While stopped on a flat surface with the engine off, feel the chain slack. Then roll the bike a little an feel it again. Do this for ten or 15 feet and see if you find that the clack is not consistent. Also look for links that don't straighten out between the sprockets.
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