Program use and permission problems on hd install

[chook]

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.

[chook]

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.