I didnt't get an exception. That would make things alot easier.
I didn't include any code since i've tried almost every example that i
could find, with the same result: _nothing happens_  The external
program never seems to get executed.
I've tried everyting from simple ones like

 try {
    String line;
    Process p = Runtime.getRuntime().exec(cmdline);
    BufferedReader input = new BufferedReader
        (new InputStreamReader(p.getInputStream()));
    while ((line = input.readLine()) != null) {
      System.out.println(line);
      }
    input.close();
    }
   catch (Exception err) {
    err.printStackTrace();
    }
 }

,to complete multi-threaded helper classes such as
http://www.codeproject.com/useritems/ProcessHelper.asp

Both of them works splendid when executed as standalone java, but not
from tomcat.
I didn't include them because i thought this was a "theroretical"
problem with running external programs from java programs running as a
windows service, not a code-error.

Please excuse my bad English.