Originally Posted by Squashman

TrueCrypt.
Works on Linux and Windows.
TrueCrypt - Free Open-Source On-The-Fly Disk Encryption Software for Windows XP/2000 and Linux

This looks like what I'm after. Do I need to make a new drive partition and encrypt and move all of my data there? Or can I encrypt the data as it is today?

But permissions should work. Not sure what is not working for you.

I want something more secure.

You could also look into use ACL's.
Introduction to Linux Capabilities and ACL's
Linux ACL - Google Search