Try using the s flag on your regular expression, to match multiple lines. The regex you are now using will not match newlines - it stops at the first one.

$input =~ s/\n/\r\n/gs;
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Also, you might try some sanity checks:

print "contains CR's!\n" if $input=~/\r/s;
print "contains NL's!\n" if $input=~/\n/s;
...
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Good luck!