I also am unable to duplicate your problem. I have displayed my input and output files with the hex conversion utility xxd (supplied with vim). I have also compared the two files with the windows file compare utility fc.

$xxd null_test.txt
00000000: 736f 6d65 2074 6578 7400 6d6f 7265 2074  some text.more t
00000010: 6578 740d 0a0d 0a                        ext....

$perl BaldGorilla.pl null_test.txt

$fc null_test.txt null_test.txt.new
Comparing files null_test.txt and NULL_TEST.TXT.NEW
FC: no differences encountered


$xxd NULL_TEST.TXT.NEW
00000000: 736f 6d65 2074 6578 7400 6d6f 7265 2074  some text.more t
00000010: 6578 740d 0a0d 0a                        ext....

$
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