Using Thompson's Water seal over a combination stain/ sealer?

Thompson's works best by penetrating the wood fibers and coating them and the spaces with a water barrier. BUT you have already applied a barrier so the thompsons will only bond with the surface.. It will not last.

If you want to use thompsons you must first remove the other stain/sealer (read the can to find out what works for that)

I guess it depends what product you used. I looked at the Pittsburgh website and can't figure out what it might have been. If the product you used was intended to seal against water, to repel water, I see no point in applying Thompson's. Your product may be blotchy because different parts of the wood have absorbed it differently. Wood is like that. What you might need is another coat of what you already used. I wouldn't expect a stain/sealer to give a fully consistent appearance or any shine, since most of them soak in. Thompson's soaks in too, so if the wood is really absorbent in some places but not in others, the same thing might happen.

I have used Thompson's with great success over an oil base stain on cedar, but that stain was intended to maintain the "new" colour of the cedar and to repel water to some extent but not to seal the wood.

get a varnish and woodstain ,combined all in one... And use that over the top.