May I suggest a change to your testing code:

# print "@firstLine1\n"; # All values print fine! MAYBE
# print "@firstLine2\n"; # All values print fine!
print '##',join('##',@firstLine1),"##\n";
print '##',join('##',@firstLine2),"##\n";
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Provided there are no '##' in your lines (showing those lines would have helped since your code is fine apart from the issue mentioned already) this will show you exactly how your arrays look like. Even better is the CPAN module Data::Dumper, especially when your data structures become more complex:

use Data::Dumper;
# print "@firstLine1\n"; # All values print fine! MAYBE
print Dumper(@firstLine1);
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PS: You could test your script with only one file i.e.  yourscript filex filex. If you still get a missing value in the output, the script is to blame, otherwise your data