I wrote this test to show what's happening:

public class TestClass {

    public static void main(String args[]) {
        testMySQLService();
    }

    public static void testMySQLService() {
        MySQLInterfaceManager mysqlInterface =
                MySQLInterfaceManager.getInstance();
        String mysqlServiceCommand =
                "cmd /c \"C:\\Program Files\\MySQL\\MySQL " +
                "Server 5.0\\bin\\mysqld-nt.exe --install MySQL1 " +
                "--defaults-file=\"C:\\Program Files\\MySQL\\MySQL
Server 5.0\\my-large.ini\"";
        System.out.println(mysqlServiceCommand);
        Process isRunningProcess = null;

        try {
            isRunningProcess =
                    Runtime.getRuntime().exec(mysqlServiceCommand);
            readStandardError(isRunningProcess);
            readStandardOut(isRunningProcess);
            isRunningProcess.waitFor();
        } catch(java.io.IOException ioe) {
            ioe.printStackTrace();
            return;
        } catch(InterruptedException ie) {
            //Assume processing has finished.
            ie.printStackTrace();
            return;
        }
    }

    /**
     * Reads the standard ouput stream of the provided Process one
character at
     * a time until the stream is closed or there is no more data.
Stores the
     * result in standardOut.
     */
    private static void readStandardOut(final Process process) {
        Thread inputStreamThread = new Thread() {
            @Override
            public void run() {
                try {
                    InputStreamReader inputStreamReader =
                            new
InputStreamReader(process.getInputStream());
                    int currentChar;
                    while ((currentChar = inputStreamReader.read()) !=
-1) {
                        System.out.print((char) currentChar);
                    }
                    inputStreamReader.close();
                } catch (IOException ex) {
                    ex.printStackTrace();
                }
            }
        };
        inputStreamThread.start();
    }

    /**
     * Reads the error stream of the provided Process one character at
     * a time until the stream is closed or there is no more data.
Stores the
     * result in standardError.
     */
    private static void readStandardError(final Process process) {
        Thread errorStreamThread = new Thread() {
            @Override
            public void run() {
                try {
                    InputStreamReader inputStreamReader =
                            new
InputStreamReader(process.getErrorStream());
                    int currentChar;
                    while ((currentChar = inputStreamReader.read()) !=
-1) {
                        System.out.print((char) currentChar);
                    }
                    inputStreamReader.close();
                } catch (IOException ex) {
                    ex.printStackTrace();
                }
            }
        };
        errorStreamThread.start();
    }
}

The output of the above is:

cmd /c "C:\Program Files\MySQL\MySQL Server 5.0\bin\mysqld-nt.exe
--install MySQL1 --defaults-file="C:\Program Files\MySQL\MySQL Server
5.0\my-large.ini"
'C:\Program' is not recognized as an internal or external command,
operable program or batch file

If I change mysqlServiceCommand to
"cmd /c \"C:\\Program Files\\MySQL\\MySQL Server 5.0\\bin\\mysqld-nt.exe
--install MySQL1";

It works as expected.

Does anyone have any idea what's going on?

Thanks

Lionel.