This is one for the almost-embarassing file …
I had no choice but to install WordPress on a subdirectory, and just changed the site URL and all is working swimmingly. However, one flaw remains: the home button goed to the WordPress URL (jms.sdsu.edu/wordpress) instead of the site URL (jms.sdsu,edu).
I have been hunting all over and I am just struggling. Any help would be most excellent, thanks!