I had a MAJOR leak last November around the seams on the side of the front cap. I had the sidewalls replaced in 2011 and quite simply, Winnebago did not get all the old sealant off the cap and sidewalls before they reinstalled and re-caulked the cap. The also did not get it properly centered and the sides of the front cap were "sprung" and fractured a plastic clip popping away from the sidewalls. The worst leak was on the passenger side roof radius curve and manifested itself with water inside from the dash to the passenger seat inside following a heavy storm. Unfortunately, Winnebago offers their 30/30 warranty (30 minutes or 30 miles) on roof caulking so you are on your own. I asked why and how the sides of the roof cap were sprung and how to repair it. They were helpful and suggested I park the coach close to a pole or large tree and use a piece of wood wedged between to hold the side tight while the caulking cured. They were kind enough to send me two replacement clips though.
The caulking they use on the roof radius and the front and rear caps is clear "Stone Mason - Gutter and Siding Sealant". It can be painted after three hours, has a 15 year life expectancy and is described as "a quick drying thermoplastic sealant". It is made by
Henry Company Canada
15 Wallsend Drive
Scarborough, Ontario M1E 3X6
www.usehickson.com.
It is sold in Canada by Home Depot for about $8.00 and their store stock is marked "Limited Supply" as I believe they are no longer carrying it. You should be able to get it from a Winnebago dealer - I got my first tube there.
Hope this helps