I think i understand why this problem occurs, but have no idea how to work round it at present.
I also have this problem and have tried PHP4 as both a CBI and ISAPI under NT4/IIS. This is what I think is happening...
Virtual directories exist only for HTTP requests. When you do an include("...") you're doing a file request so PHP is going directly to the file system right? That's why it can't open the file as the directory simply does not exist.
e.g. i have two sites each have a folder (i.e. sub site) in iis.
The first is called test1, the second test2.
test one has a sub folder "includes". in the root of test1 this would work
include ("./includes/allinc.inc");
so i create a virtual dir for test2 and point it to includes in test1. if I then do the same include from the root of test2 it does not work.
What else can we do... anyone?