In Windows, does MagicISO add itself to the menu? I think (I could be wrong) that winemenubuilder reads what the app would insert into the Windows menu and translates that into a Gnome or KDE menu entry, but if the app doesn't add a menu entry for itself in Windows, Wine couldn't do it either. Have you tried installing any other programs in Wine to see if they get added to the Gnome menu? The one other thing I can think of is, have you manually added any entries directly under Wine in the menu hierarchy (rather than using the convoluted array of submenus it like to create)? I found that in KDE doing that has prevented Wine from ever adding another entry to my menu. (Which is fine with me; I never wanted all that crap in my menus anyway.)
