Thank you Shane, and Greetings!
As I said, the program in Beta that I ran was Tweaking.com Beta.
It is only shortcuts that come up as black squares, and the matter is not problematic, as the black square changes to the correct icon as soon as it is placed on a dock or menu. But on the desktop it remains a black square, which, oddly enough, opens the relevant program if clicked.
I think I know the answer. It seems that, as I am using a wallpaper from Documents at the moment, and not from Microsoft's themes, Microsoft themes is causing the black square. I'm not sure how to do a fix, but I'll give it a try.
Thanks again and best regards.