A good module that does similar things is File::Find. If you get really stuck, you might take a look at its guts. As to your two questions:

1. There shouldn't be any file system level differences... it's more likely you've accidentally used an option which isn't supported on ActiveState's interpreter for 9x. (fork() and alarm() come to mind)
2. The -X test will help you here. Specifically:

   if (-d $filename) {
       print "$filename is a directory.\n";
   } else {
       print "$filename is a file.  Skipping...\n";
   }
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