Strange thing is that the BOM is in ISO-8859 representation. In other words it shows up as .

Actually, those three bytes (EF BB BF) is the UTF-8 encoding of the BOM (there is no ISO-8859 representation of the BOM).

As Perl doesn't automatically add a BOM with UTF-8 files (at least I've verified it doesn't on Unix, and AFAIK, Perl doesn't behave differently on Windows in this regard), I suspect the BOM already is in the data you're writing out.  Where does it (the $_ in your case) come from?

In this case, you could remove the BOM with:  s/\x{feff}//;