I realized what my issue was and resolved it. I figured I would let everyone know how a simple mistake can drive one insane.

With other distros of Linux I always ran LimeWire from a terminal session, using SU. It just so happens that right after I setup security for Apache I tired launching LimeWire from within GNOME, as my user. I made a rookie mistake and assumed the reason it would no longer accept the download directory was due to the security settings having been changed within Apache, however, it was due to the following.

I setup the directories within Apache as SU, for security reasons....go figure. When I would lauch LimeWire from a terminal session it just so happens I was always already in a SU session as I would be doing some work on the box and deside to lauch LimeWire for some downloading. When I launched LimeWire as my user, via GNOME, LimeWire did not have the rights it required.

Pretty simple in the end...only took be a couple cups of coffee before I leaned my head to one side and said, "...wait a minute here..."