Hi,
I had a problem with a similar mouse like you. (I claimed it was a three-button, when actually it was a four-button one. For third button push the scroll wheel! ) Mine is a PS/2 one, but I used it with an USB adapter, too. In neither case I could, concerning pro/E, get the thumb button work as the by Logitech Mouseware assigned Strg-key.
Maybe there is a setting in some configuration files, but I don't know this.