It looks like there is a bug for setting multiple include_path for php that run at windows server.

For php that runs at non windows server:
you can set
include_path	= .:/www/includes:path3
and when ever we use include it will always look for all the path starting from . and /www/includes and so on. If you specify your own path at include statement, eg: include "/test/test.php";
it will be found at "./test/test.php".

include_path	= c:\www\root\includes
single path works find with windows server.
I have problem when trying to set multiple path. 
As the php.ini comment:
include_path	= .;c:\www\root\includes
won't works (may be anything after ; are comments!)

However I can go around this by specify 1 include path and always use "." whenever I use include statement.
eg include "./test/test.php";