i believe that Colin's message means php-start-end simbols must apear on includes,
are you using it?
main.php contains
(?php // ~ start php code
include 'code.inc.php';
foo($a);
?> ~ end php code
code.inc.php contains
(?php
include 'vars.inc.php';
function foo($b) {
echo '$a = ', $b;
}
?)
and vars.inc.php contains
(?php
$a = '-pi';
?)