persistent home & permissions

Ever Since I created a persistent home, config, and swap file my hard drive can be written to. Even though it says that it isn't writable. Owner and Group show up as knoppix. How do I put it back to no access for everything but my home/config/swap?

I've tried going to properties>>permissions on hda1 and setting everything to read only but it doesn't seem to have an effect.

**Also note that the files on my hda1 do not all have the same permissions. for example:
Program Files has r-xr--r--
zope-instance has rwxr--r--
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--thanks for any help you can give.