Without a small sample of your input file, it is not simple to reproduce your results. Try to print both values before your "if" line:

print "julday >>>$julday<<<\n";
print "julday_old >>>$julday_old<<<\n";
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Are these values integers, or are they floating point values?

Isn't...

  if(! ($julday == $julday_old)){
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the same as...?

  if ($julday != $julday_old){
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