With 1.7.1 and also with svn 2011-04-13 revision 763 i get these warnings:

/tmp/doxygen/test.php:24: warning: documented function `$ref' was not declared or defined.
/tmp/doxygen/test.php:27: warning: documented function `$ref $data' was not declared or defined.
/tmp/doxygen/test.php:30: warning: documented function `$ref $data' was not declared or defined.
/tmp/doxygen/test.php:16: warning: Member e(&$ref, $data) (function) of file test.php is not documented.

Unedited Doxyfile from doxygen -g, test.php looks like this:

<?php
/** @file */

/** func a */
function a ($data) {}

/** func b */
function b ($data, &$ref) {}

/** func c */
function c (&$ref) {}

/** func d */
function d (&$ref, $data) {}

function e (&$ref, $data) {}

/** @fn a ($data)
append a works */

/** @fn b ($data, &$ref)
append b works */

/** @fn c (&$ref)
append c fails */

/** @fn d (&$ref, $data)
append d fails */

/** @fn e (&$ref, $data)
func e also fails */

?>

Both html and latex output lack "append c fails", "append d fails" and "func e also fails".