Is there any way to send screen shots?

Better just to get perl to tell you what's in the file.
As Athanasius suggested, I suspect that the file really does contain a NULL, and the tool you're using to look at it converts it to a space.

On Windows 7 (perl-5.28.0), I created a file (null.txt) by running:

C:\_32> perl -e "$s = 'x' . chr(0) . 'y';print $s;" >null.txt
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I then examined the contents of null.txt by running:

C:\_32> perl -le "open RD, '<', 'null.txt'; $x = <RD>; chomp $x; print
+ ord substr($x, 0, 1); print ord substr($x, 1, 1);print ord substr($x
+, 2, 1); print length $x;"
120
0
121
3
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After using your script to create null.txt.new, I then ran the same one liner to ascertain the contents of null.new.txt

C:\_32> perl -le "open RD, '<', 'null.txt.new'; $x = <RD>; chomp $x; p
+rint ord substr($x, 0, 1); print ord substr($x, 1, 1);print ord subst
+r($x, 2, 1); print length $x;"
120
0
121
3
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So it looks to me that I also am unable to reproduce the problem.

Cheers,
Rob