Why should JavaFan have to prove anything to you?

You have not shown any self-contained code of how you run Perl. Maybe you could start debugging your environment by removing Perl from the equation and running cat? Maybe you could eliminate the operating system from the equation by running your code on a different OS? Java is supposed to be cross-platform and Perl is likely installed on all machines already anyway.

As Perl is called from other programs quite regularly to have its output post processed (for example, served via a webserver), I would think that it is far more likely that the error is somewhere in the calling code than in how Perl produces its output.

You could redirect the Perl output to a file from a shell script and call that shell script from Java. Afterwards, you could read in the output file which was created.

Start showing some effort and do the work that only you can do.