I can't say I have had this problem really. After you do your usual clean up you could try to do another chimney of charcoal without any food in the grill and see if it would burn out any remnants that could be contributing to your flavor issues. If it is really bothering you and you have the space you could also try utilizing certain grills for different types of cooks. For instance I have a kettle that I only use for pizza cooks because they high heat is hard on porcelain finishes, I have a ranch that I use when I am cooking large amounts of food or entertaining a group of people, and then I have my Performer that I use for just the household.
Not sure that either of these options are the answer, but it is something to think about at least.