So, I got a lot of responses to my earlier post about using a WS under a virtual host. The recommendations pretty much centered around adding an alias to my jrun-web.xml file. This, however, didn't help. Another user suggested that maybe my folder structure was causing the issue - I had used dots in my main folder (tasktracker.jedi.com). However, switching to a simpler folder name didn't help.
On a whim, I decided to try switching to a new machine. This was a pure install of MX - no hotfixes, nothing. Under there - it worked perfectly - with no mods to any XML file or to anything else.
So, now I'm not sure what to do. I may consider simply applying the hotfixes to the second computer to see if it corrects the issue.
I'll post again when I find out more.