At the very least you are missing a closing curly brace at the end of the while loop.

Most probably you do not need the &-sigils in the subroutine calls (if you do not understand why you do not need them, then it is almost certain you do not need them, otherwise have a look at perldoc perlsub).

Other than that, your program seems to work, BUT:

• You are not printing to a file, so how could you check that all output was on one line? Did you redirect STDOUT perhaps in the shell?
• How can you see the output from your perl-script in the PHP page? What is the mechanism to transfer the perl-script's output to PHP?

My guess is that you have to look at the interface between the perl-script and your file and/or PHP page and that somewhere there the EOL-characters get messed up.