Ive gone through and put print's throughout the script and ive finaly found out the problem! its the bloody matching string. there is something in my reference file that matching each time it reads the data file
i did a:

 if($s_line =~ /$str/){
    print "$str -- match\n";
    } else {
    print "$str -- no match\n";
    }
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on my test data and it shown that its matching an empty line so there must be something in my reference file thats matching up (ive already checked and its not empty lines). I'm gonna look for it now so i wont keep you hanging on, but cheers for all the improvement suggestions. Im going to go through them all when I have more time and no deadline to catch
cheers for the help!
in heinsight, I should have given better examples at the start. sorry. will do next time