Sounds like your motor has a little built up unburnt fuel in it. Do you ever run your motor hard for 15 to 20 minutes periodically (say every few weeks)? When I mean hard, I mean under load at near full throttle. I also have a Yanmar and find that I don't run it hard every month, when I do throttle up for the first few times, I get a blueish smoke for few seconds and some sooty water.
Next time you lave that dock, and it is safe, engage the motor and run it a near full speed for 10 to 15 minutes to see if that helps.