Yes, I believe that Cramej is correct and that HR-U has emulsion on both sides. However, it may be the opposite problem: the pockets hold more developer and thus that section of the negative is darker. I doubt that you can fix this with agitation.
It may be my imagination but I think I can see the texture of the tray on the negative in some places. You could try putting a thin sheet of glass or even a scrap sheet of film on the bottom of the tray to provide an even surface. (It's probably a long shot.)
Frankly, I'd also worry about scratching the bottom side of the negative (a common problem with double sided film, even just loading the camera's film holders.)