When using php's debug use flag, xdebug won't work with the configuration supplied by the ebuild. The file /etc/php/cli-php5/ext-active/xdebug.ini has the line > zend_extension= but needs to be > zend_extensin_debug= since debug is enable for php. Otherwise xdebug will not be loaded.
This is fixed in the current eclasses, if debug is enabled you will get zend_extension_debug, and if threads are enabled, you'll get the appropriate threaded-ini-entries. Best regards, CHTEKK.