Id that really the actual code & input & output, because they don't seem to match up:
1 : /DIR9/ParentNew/Child1 : /DIR8/Docs/ParentOld/Child1
has 3 ':', yet none of them appear in the output, in spite of the fact you split on tabs.
Are the tabs at the start of each dirpath? It would be much better if you showed the input/code/output inside LQ code tags..
The missing C is probably because you have an invisible ctrl char (a 'del') at the start there. Just manually delete the 1st 3 chars of "Comparing" and re-insert carefully.
Also, the word 'and' in your code
print "Comparing entries $DataString: $DataString and $DataString \n";
is entirely absent from the output.
Show us the real stuff.
Also, always start all Perl progs with warnings and strict modes on: