im sure they meant to use absolute file paths for all the files.
an easier way to make your file paths absolute would be like so
include ($_SERVER['DOCUMENT_ROOT'] . '/path/to/script.php');
btw- including a file should NOT change php's current working directory. the only way that gets changed is if there is a call to chdir() somewhere.
but, there was a member on another board who was having this problem. we went through all the possibilites and it did appear that included files in different directories were changing php's current working dir. you may want to check bugs.php.net for your version of php.