Not necessarily anything to do with STDIN/STDOUT, this goes through double encoding and no decoding as well:

open(INPUT, "<input");
open my($in), "<&:encoding(japhy)", "INPUT" or die $!;
open my($out), ">&:encoding(japhy)", "STDOUT" or die $!;
print $out $_ while <$in>;
close(INPUT);
[download]

The output is:

> < abc
> < def

Update: Confirmed that it works fine if you call binmode afterwards. It looks like this bug: http://rt.perl.org/rt3/Ticket/Display.html?id=34595