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There should be a more recent (and improved) version of that Batch file in the resources sub-folder in the Calibre install folder.
You would need to check through it that the paths are correct for your setup.
Note that as long as Calibre is on the system search path it will be found regardless of the current folder at the time you run the batch file. If it is not on the system search path then you want to make sure that the batch file sets the correct location.
However I am not sure why you should ever get the symptom you mentioned of lots of DOS boxes opening up when it does not work!
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