Okay, in the end I used strat's line of code within a loop to test for each directory.
I tried crazyinsomniac's code, which only printed out one filename in a directory not even included in the path. I probably used it wrong!
So anyway, thanks a lot for your help (and that includes everyone that posted).
I would post the code I now use, but it's quite long... And sorry about the use of HTML there... I noticed that it shrunk the size of the nodelets after I posted it.

Update: Okay, I tried crazyinsomniac's code again, and it worked for the most part, but it still left valid directories out of the options, so I went back with strat's code with a small modification. Here is the code I use now:

my $root_path = "C:/Apache/www-root";
my $count = 0;
my $dir = "";
my @dirs

find(\&{ sub {
     if (-d "$File::Find::dir/$_"){
          if (++$count == 1) {
               push @dirs, $File::Find::dir;
          } else {
               push @dirs, $File::Find::dir . "/" . $_;
          }
     }

   }
}, "$root_path");

foreach $dir (@dirs) {

     my $tmp_dir = $input{'file' . $i};
     my $tmp_dir =~ s/(.*)\/(.*)/$1/;

     if ($test_this_directory !~ /^\Q$full_file_path/ && $dir ne $tmp_
+dir) {
          #valid directory - add it to cpoy options
     }
}
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