I hit this PHP bug: http://bugs.php.net/bug.php?id=34552 when trying to install Moodle on my laptop, and it took me ages to find that this was the problem.

Basically, if one of the folders above $CFG->dirroot has 'x' but not 'r' permission for apache, then require_once can't work out the canoncial path for files and some files can get included more than once.

However, that took a lot of working out, because the effect of the bug was that on some pages, but not others, moodle just gave no output.

To test for this, I think you just need to do realpath('.'), and see whether that looks like $CFG->dirroot . 'somthing', or './somthing'.