opendir($DIR, ...) doesn't work because lexical filehandles weren't available in perl 5.004. But opendir(DIR, ...) doesn't work either, because your checkDir subroutine is recursive, but you're sharing the same filehandle between all subroutine calls.
You can get around this by reading the entire directory (i.e., get the full list of filenames in the current directory) before your recursion step.
On a side note, your example is way, way longer than it needs to be. Boil down your example into the smallest bit of code that reproduces your problem. In so doing, you might have noticed that it only happened when you tried to do it recursively.