Clint,
Sounds like you have the proper rubbers then!
The way the upper and tailgates work has to be one of the worst production vehicle designs of all time, with the top closing first, and the bottom forming an overlap that naturally deflects water in, rather than out.
The lower tailgate rubber is glued in across the top of edge of the frame. It has quite distinctive moulded corners that turn down about 80mm at each end. (Will take a photo next time I'm at the shed)
The other rubber fits in the channel around the whole opening, as per the following photo.
Fortunately, the reproduction rubbers available from Rare Spares actually fit really well, and provide a solution that is at least as good as the factory.
If you post a picture of the top edge of the lower tailgate, I can advise whether you have the correct set up.
Regards
Edward