OK, you're on a unix box, so using "chop" instead of "chomp" is not a problem (but it is depricated, IIRC). I think you made a mistake copying the code into the post -- there's a problem in the section shown below, which I have commented (but if the code really looks like this, maybe this is part of the problem):

 foreach $loop (sort `cd $data_dir; ls -d *`) {
     chop($loop);

     foreach $loop2 (sort `cd $data_dir; ls -d $loop/*`)
     {
         chop($loop2);

###      foreach $loop3 (sort `cd $data_dir; ls -d $loop2/*`) {
## should be:
##       foreach $loop3 (sort `cd $data_dir/$loop; ls -d $loop2/*`) {
## or:
         foreach $loop3 (sort `cd $data_dir; ls -d $loop/$loop2/*`) {
            chop($loop3);
## BTW, this:  $all_files[$i++]=$loop3;
## should be:
            push( @all_files, $loop3 );
         }
     }
 }
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Apart from that, you're doing  $data_path = s/[\n\r]//g; which seems unnecessary -- you already chopped it in the loop above, and it's just a line of output from "ls".

Then you're splitting $data_path on slash characters, which would never be present in $data_path given the code as posted, so $blank and $file are always empty strings, I think.

I didn't see where &get_key_field() is defined; are you confident about what it's return value is, or should you be testing that?

I'm sorry if this is all peripheral to the real problem, but I think it's worth looking into -- try "perl -d" on the script, set some breakpoints at key lines, and step through it to see whether the values of the variables match your expectations.