I don't know much about pseudo terminals. Just for curiosity, I tried your code on a Linux machine. I had to modify == to eq to prevent lots of warnings. I also get a different output if I change chomp to s/\s+$// (there was "\r" present). To reduce the output, I also print only if length $line. 2, 4, and 6 never get to the output, but sometimes, I get something like:

TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 3
TIME: Fri Jul  4 08:38:34 2014 OUTPUT: 1
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Something weird's going on.