I've had an Advance cover on my 01 Trac since right after I bought it in early 02. Through car washes, thunderstorms and even a tropical storm, it has never leaked a drop. The only water I've ever seen in the bed at all was when i splashed through a deep puddle and it splashed up through the drain holes in the bed. (There are plugs available for those through someone on the site, if you think it's important.)
I've been extremely happy with the cover's look, locking mechanism and ease of removal. I have only two criticisms of it: 1) The aluminum it's made of dents fairly easy if you're careless with it. I accidentally left my keys on one side of the cover, opened the other side all of the way and now have two matching dents where the cover came together over my keys. 2) The spring latches make it very difficult to open either side of the cover with one hand. If you're holding something you want to put in the bed, you have to put it down, open the cover, pick it back up, put it in the bed and then close the cover again. Neither is a major issue, just two things I've noticed in my years of having it.
EDIT: One other minor point. You can't open and close the tailgate with the Advance cover shut, as it pinches the rubber flap that extends over the top of the tailgate. (Don't know if you can do so with the Ford cover or not.) Again, not a big deal, but just in case you will need to take things in and out of the bed via the tailgate often, I thought I'd throw it out there.