virtual directory use

I'm designing a Drupal site for a University that also uses virtual directories based on the Center's base url:
(current site -- not drupal based):
base url: www.scalemsp.org
virtual directory: www.wcer.wisc.edu/scalemsp

when I test the virtual directory in development it doesn't work, I receive several PHP error messages, the first one is:
undefined index....\bootstrap.inc on line 611
(and there is another one for line 551)
and these are followed by the usual cannot modify header information....

I'm not familiar with virtual directories, so I'm conveying info back and forth about Drupal to the web staff.

Any help would be appreciated so we don't have to use redirectors!!