Why not just change main menu acordingly (simulate tree like structure). You would always expect aditional filters if any directly under the Download text itself.
Also adding Download links on game/program description pages would be usefull.

I must admit that I also couldn't get to programs download link. Even after reading your post it took me some time to figure it out.
The problem is that both main menu and submenu shape is the same therefore they seem to be of equal importance and look more like two seperate section of the main menu.