To get more specific help, you should update your post with a small sample of your input files (a few lines each), your actual output and your expected output.

Probably unrelated to your problem... if you are interested in using a more robust (and modern) Perl coding style, run your code through perlcritic. Here are a few of the issues:

'Bareword file handle opened at line 37, column 2.  See pages 202,204 
+of PBP.  (Severity: 5)',
'Two-argument "open" used at line 37, column 2.  See page 207 of PBP. 
+ (Severity: 5)',
'Close filehandles as soon as possible after opening them at line 37, 
+column 2.  See page 209 of PBP.  (Severity: 4)',
'"$nm" is declared but not used at line 27, column 1.  Unused variable
+s clutter code and make it harder to read.  (Severity: 3)',
'Mismatched operator at line 53, column 21.  Numeric/string operators 
+and operands should match.  (Severity: 3)',
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