Program use and permission problems on hd install

I'm running Knoppix STD 1B off my hard drive. I've noticed however, with many programs, they don't work from the Knoppix toolbar shortcuts, I have to manually open their executable from /usr/bin. Some files don't even work then - I have to open them from a console, and even then I have to change to root before it will let me open it. I've tried changing the permissions to 777 while logged in as root, but I still can't simply click to open it. I don't even get a notification box telling me I don't have the right permissions, it just tries to open it for a bit, then nothing happens. I've tried reinstalling a couple times, but the results are always the same.

If this helps at all, EtherApe is one that works straight from the desktop menu shortcut, Cheops is one that works only while su in a console.