I've got a bit of an issue with Aptana that's causing a message regarding permissions to come up while it's loading. If I run nautilus with root permissions I don't get the message while Aptana's loaded.

I've tried extracting Aptana to the /opt directory, and to my home directory with the same results.

I noticed after I ran Aptana that an empty Aptana directory appeared the /root directory. Could the problem be that Aptana is trying to write to that directory or something?

Here's the message I get,
Could not initialize the application's security component. The most likely cause is problems with files in your application's profile directory. Please check that this directory has no read/write restrictions and your hard disk is not full or close to full. It is recommended that you exit the application and fix the problem. If you continue to use this session, you might see incorrect application behaviour when accessing security features.