Here's my checkin.php, which works ok for me. I apologize if the text gets garbled. My personal patch is between the line "START CUSTOM" and "END CUSTOM"

<fixed>
#!/usr/local/bin/php -q
<?

Mantis - a php based bugtracking system

Copyright (C) 2000 - 2002 Kenzaburo Ito - kenito@300baud.org

Copyright (C) 2002 - 2007 Mantis Team - mantisbt-dev@lists.sourceforge.net

Mantis is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 2 of the License, or

(at your option) any later version.

#

Mantis is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

GNU General Public License for more details.

#

You should have received a copy of the GNU General Public License

along with Mantis. If not, see http://www.gnu.org/licenses/.

    # See the README and LICENSE files for details

    # --------------------------------------------------------
    # $Id: checkin.php,v 1.5.2.1 2007/10/13 22:35:16 giallu Exp $
    # --------------------------------------------------------

    global $g_bypass_headers;
    $g_bypass_headers = 1;
    require_once( dirname( dirname( __FILE__ ) ) . DIRECTORY_SEPARATOR . 'core.php' );

    # Make sure this script doesn't run via the webserver
    # @@@ This is a hack to detect php-cgi, there must be a better way.
    if ( isset( $_SERVER['SERVER_PORT'] ) ) {
            echo "checkin.php is not allowed to run through the webserver.\n";
            exit( 1 );
    }

    # Check that the username is set and exists
    $t_username = config_get( 'source_control_account' );
    if ( is_blank( $t_username ) || ( user_get_id_by_name( $t_username ) === false ) ) {
            echo "Invalid source control account ('$t_username').\n";
            exit( 1 );
    }

    if ( !defined( "STDIN" ) ) {
            define("STDIN", fopen('php://stdin','r'));
    }

    # **** START CUSTOM ****
    $t_cvs_user = exec("whoami");

    # Detect references to issues + concat all lines to have the comment log.
    $t_commit_regexp = config_get( 'source_control_regexp' );
    $t_commit_fixed_regexp = config_get( 'source_control_fixed_regexp' );

    $t_issues = array();
    $t_fixed_issues = array();

    $t_comment = $t_cvs_user.": ";
    $t_line = exec( "cat $argv[1]\n" ); # line added + modified
    $t_comment .= $t_line;

    if ( preg_match_all( $t_commit_regexp, $t_line, $t_matches ) ) {
            for ( $i = 0; $i < count( $t_matches[0] ); $i++ ) {
                    $t_issues[$i] = $t_matches[1][$i];
                    echo "found issue: ".$t_issues[$i]."\n";
            }
    }
    if ( preg_match_all( $t_commit_fixed_regexp, $t_line, $t_matches ) ) {
            for ( $i = 0; $i < count( $t_matches[0] ); $i++ ) {
                    $t_fixed_issues[$i] = $t_matches[1][$i];
                    echo "fixed issue: ".$t_fixed_issues[$i]."\n";
            }
    }
    # **** END CUSTOM ****

    # If no issues found, then no work to do.
    if ( ( count( $t_issues ) == 0 ) && ( count( $t_fixed_issues ) == 0 ) ) {
            echo "Comment does not reference any issues.\n";
            exit(0);
    }

    # Login as source control user
    if ( !auth_attempt_script_login( $t_username ) ) {
            echo "Unable to login\n";
            exit( 1 );
    }

    # history parameters are reserved for future use.
    $t_history_old_value = '';
    $t_history_new_value = '';

    # add note to each bug only once
    $t_issues = array_unique( $t_issues );
    $t_fixed_issues = array_unique( $t_fixed_issues );

    # Call the custom function to register the checkin on each issue.

    foreach ( $t_issues as $t_issue_id ) {
            if ( !in_array( $t_issue_id, $t_fixed_issues ) ) {
                    helper_call_custom_function( 'checkin', array( $t_issue_id, $t_comment, $t_history_old_value, $t_history_new_value, fa

lse ) );
}
}

    foreach ( $t_fixed_issues as $t_issue_id ) {
            helper_call_custom_function( 'checkin', array( $t_issue_id, $t_comment, $t_history_old_value, $t_history_new_value, true ) );
    }

    exit( 0 );

?>
</fixed>