Mark,
Mine has had the same seams since we have owned it... It's an 01 we have had it since 06.
They do seem to vary a bit with temperature, if it is colder out they are less pronounced, but even at their highest point I wouldn't consider them major. Almost every Winnie I have seen has been the same so I never really gave it a second thought. Yes, I am pretty anal about cleaning the roof too, so I am up there at least 4 times a year washing and waxing....
I chock it up to flex and heat expansion. Have you ever seen Vinyl siding installed on a house? You can't nail it 'Tight' because when the sun its it it must expand or contract. Since the fiberglass used on our roofs and sidewalls is really nothing but a thin layer, I think there needs to be some expansion in that too, maybe not as pronounced as vinyl, but it still moves some...
John