And I don't think the original poster was asking about Perl programs written in the command line, only about programs run from the command line.

It might be a line-ending problem of another kind, but I second the "please provide examples" post above.

Just to note, this isn't MacPerl any more, it's just ... Perl running on MacOSX. OSX is UNIX-like.

That's what I thought, but wasn't sure; hence the Mac perl, not MacPerl. Are there editors that have \x0D as newline convention while the OSX perl is expecting \x0A? Or vice versa?

And I don't think the original poster was asking about Perl programs written in the command line, only about programs run from the command line.

It might be a line-ending problem of another kind, but I second the "please provide examples" post above.

If it is a line-ending problem, pasting an example will probably hide the evidence. Maybe stick something like

BEGIN { use Data::Dumper; $Data::Dumper::Useqq=1; open FOO, $0 or die 
+"nope: $!"
; print Dumper $_ while <FOO>; exit }
[download]

at the beginning of the source and run it and show the output. I don't remember if the Data::Dumper in 5.6.0 had the Useqq option, though.