If you do not want to raise an issue, then I am afraid it is much harder to progress it unless the problem is obious - and it probably is not as I can run batch mode with no problems.
Strange about the program you mention is running - it should not be running javaw.exe but java.exe in batch mode.
There MUST be a confguration file somewhere as it is set up and used by the GUI. The location can be found from the Help menu in the GUI. If somehow it does not exist (or is not found) then the batch mode will definitely fail. The same should apply to the log file. You could also get a batch mode fail if you are not running under the same user as was used for the GUI as the configuration file is stored at the user level unless you give over-ride parameters for its location at run time.
If you start the RUN.CMD file from a DOS window while located in the Calibre2Opds install folder you may well get some useful information displayed about the startup process which could give an indication as to why things are not working.