I suggest trying the script from Re: cgi/perl/fortran web program, calling it with both methods and comparing the outputs. (perhaps extended like below)
use strict;
use warnings;
my $n; 
print "Content-Type: text/plain\n\nPerl Version $] ($^V)\n";
print "ARGV" . $n++ . ": >>$_<<\n" foreach @ARGV;
print "\n$_:\n", qx($_ 2>&1) foreach qw(id pwd env);

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In reply to Re: Perl script works differently from Apache then CMD line by soonix
in thread Perl script works differently from Apache then CMD line by IT_not_Dev

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