We have an '05 V-Ride, and have not had this issue. We store ours outside and have not had an issue with the cover, but then our cover is that generic off-white color. Maybe if you have a colored cover, the color would bleed through after a rain, and then the sun sets it in?? But then, why wouldn't it stain everything? Hmmm.
By the by, what is a "reflash"? We've set PP as low as 7ish mph, and have had no problems.