Paolo,
If you are running under Linux, the lowercase pdfreflow command should run the command line interface. The GUI is in PDFReflow.jar, and requires you to run it as:
java -jar PDFReflow-0.8.6.1.jar
Could it be that you have another pdfreflow command? In the terminal, type:
which pdfreflow
type pdfreflow
to see the full path of the the command line.
If you created a shell script to invoke the GUI, this could be the problem. The lowercase pdfreflow command must be in your path, and it must the the command line version.
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