phpGroupWare, which works under 6.2 using relative paths ex. include("inc/config.inc.php"); fails unless you specify full path ex. include("/var/www/html/phpGroupWare/inc/config.inc.php");
The default include path (which is set now, while it wasn't before) no longer includes ".". Change your include statement to "./inc/config.inc.php", and it should work again. The next build of PHP (4.0.1pl2-6) will include the current directory in the include path again. Please reopen this bug ID if you find that this is not the case.
Or, change the include_path set in /etc/php.ini from "/usr/share/php" to ".:/usr/share/php", which is the fix the next build has.