What do you expect if($lines[1] != <FILE2>){ to do?

Always use strictures (use strict; use warnings;)!

!= will unmify the strings on either side of it, most likely to 0, which is hardly what you might desire. != provides a scalar context for <FILE2> so a single line will be read from FILE2 for each iteration through the while loop, regardless of any synchronization issue that may be caused by extra or missing lines in either file.

True laziness is hard work

In reply to Re^4: Read two files and print by GrandFather
in thread Read two files and print by sandy1028

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