$VAR217 = 'MS01-9167-A7-DCIS';
';AR218 = 'MS06-1878-D2-DCIS
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If this is exactly what you get from data dumper, then there is a carriage return at the end of the line (hex 0D).

It might mean that you use a msdos file on unix and your chomp only removes the Line Feed and not the Carriage return . See the man page of chomp and its dependance on $/. Setting $/ to "\r\n" would correct that, but then real unix files would not work. If you need both file types to work, use a regex instead of chomp

About GrandFathers suggestion: Is the ordering of both files important to the result? If not you might put the second file into a hash instead of the first. But if you want helpful answers to that question you might open a new thread and tell us exactly what you want to do with those two files