My totally unscientific, pulled-straight-out-of-my-arse speculation: about 65% design, 35% break-in. It (thankfully) never goes away. Definitely one of this bike's endearing qualities.Mine has the whine as well, most noticeable at low RPMs. It seems much louder at idle when the engine is cold, but once it heats up, the whine isn't quite as loud. I really don't notice it too much once I get moving. I'm only a little over 200 miles right now. Question to the fortunate folks who have more saddle time on the CTX 1300 than I have: How much of the whine is would you say is due to design, and how much is due to my engine not yet broken in?