Then how does your "main program" call the "subprogram" during the test -- how is your test script interfacing with the webserver? Is the "main program" also on the webserver, and if so, is it calling the "subprogram" as a function call, or thru a system() or `` access, or something else? Or is the "main program" on your local machine, accesssing the webserver "subprogram" via LWP::Simple? Or something else entirely?
Since it's printing to STDOUT to the web browser, are you sure you've not accidentally embedded the "subprogram" output inside something hidden in the HTML? Could it be inside a comment, accidentally inside a tag, or in a non-displayed element? (view-source is your friend when a CGI's output is not where you think it should be).
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