Ok. If you use the batch file now, it automatically tries to start the game even after the patcher has auto started. Result = 2 copies of GC trying to open at once.
To fix this: Add a 'pause'
@@echo Now Loading Patcher.
@@echo Close the patcher when it is done, to continue.
@@echo Copying Updated Sound to SoundE Directory
@@copy Sound*.kom SoundE /Y
Here, the bolded underlined bit. Then the script will not progress unless you hit a key. Wait for the patcher to launch GC and simply close GC, then go back to the dos prompt and press a key.