The flaps that Edge is talking about do not exist on your 2005 Sport Trac. They are little diverters that direct any water getting past the seals at the outer edges of the hinge will be directed over the bed rails. They are easily lost when the tonneau cover is removed or pop out occasionally when the cover is opened.
Covers manufactured in 2002 and later do not have the same center hinge seals and do not use those diverters. Look in my library. I have a document in there that tells you how to get your tonneau cover to seal better. It was written for people with the LeverLift or EZLift tonneau cover lift kit, but the general principles apply to covers without the lift kits.
...Rich