Usually this kinds of problems turns to be something else that we haven't considered, and probably you already believe that is something wrong with the open ( which might be or not ) and you focus only on that.

Try to write a shorter program that only opens a directory and see if that removes everything, ... or run your program using the debugger with perl -d your_program.pl and check if after each step the directory gets wiped out, if so you'd find the line that did it and you'd be available to write a minimal program that evidences the bug ( or new test case for perl 5.12.X :D )