[ BUILD # : 201308222300 ]
[ JDK VERSION : <1.7.0_21 ]

Following sample code snippet reproduces the issue:

        function bogus($asd) {
            for ($i = 0; $i < $asd; $i++)
                if ($i == 3)//bla bla bla
                    return false; //bla bla
            return $i;
        }

Hitting SHIFT+ALT+F you get

        function bogus($asd) {
            for ($i = 0; $i < $asd; $i++)
                if ($i == 3)//bla bla bla
                    return false; //bla bla
                    return $i;
        }

which is wrong.
On the other hand, if you remove the last comment and invoke autoindetation
again, indentation is applied properly:

        function bogus($asd) {
            for ($i = 0; $i < $asd; $i++)
                if ($i == 3)//bla bla bla
                    return false;
            return $i;
        }