Just for kicks, try changing line the first 3 lines to...

#!/usr/bin/perl -w

open (IN, "one.seq.one.line") or die "can't open IN: $!";
open (OUT, ">out.index.pl") or die "can't open OUT: $!";
print OUT scalar(localtime), "\n";
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..then check to make sure that when you run the program, it doesn't die, and the date stamp gets written to you output file.

I suspect your code works fine, but the OUT stream isn't getting opened correctly and you just keep looking at an old version of the output file.

that's just my guess.