Nothing jumps out at me as being wrong in your code, but I do have some stylistic things and best practices you might want to consider...

• You should really be checking the success of your open calls. Also, most people will suggest the three argument form of open and lexical file handles: open my $out, ">", "$resultsfile.corrected" or die "could not open $resultsfile.corrected: $!"
• You don't need to use printf at all in this code. Using print and string interpolation is usually easier to read: print $out1 "$julday_old $day_cnt\n"
• I think that if (! ($julday == $julday_old)) would be better written as if ($julday != $julday_old)

OK, enough of my opinions.

So the only real question I have is, are you sure that block of code is being reached? I assume you're seeing the printouts to the console, but I just thought I would ask.
Update: I reread the question and saw that the prints are showing up on stdout. I'm out of ideas...

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