This is a classic:  CR-LF versus LF newline differences in text files between operating systems (DOS/Windows versus Unix/Linux/OS X).

What text editor did you use to save the file using those formats and character encoding names? I ask this because those names are bogus and confusing, especially the character encoding names. There's no such thing as an encoding named "DOS", and the name "ANSI" is a historic misnomer that is more properly "Windows-1252" or "Code Page 1252" or "CP1252". I suspect the encoding name "DOS" is intended to mean "Code Page 437" or "CP437". But who knows?

You may need to use a better text editor.

Unless you're doing something extraordinary to thwart its default behavior (setting the mode of the I/O layer to :raw, for example), Perl should just be doing the right thing with the line terminators in your file. In other words, in general, Perl handles both CR-LF and LF logical newlines correctly and transparently. What version and distro of Perl are you using? ActiveState Perl? Strawberry Perl? Or the Perl that comes with Cygwin?

Jim