We don't know what you did in either program of course. My first instinct would be to try

./perlscript.pl > output.txt 2>&1
[download]

and see if the output magically appears in the file. If so then you can conclude that the output is going to STDERR instead of STDOUT as you expected.

Update: and if that doesn't do anything also try 0>&1 just to make sure and if that makes the difference you were writing to STDIN.