++ for tracking this problem down and for reporting your findings here. Perhaps it will help someone out in the future.
By the way, I went back and analyzed your code using perlcritic, hoping that it would detect and report an opendir without a matching closedir.
No luck -- at least not with its default settings. Perhaps it can be configured to catch this type of situation.
I believe this problem can be averted using the File::Slurp module from CPAN. Its read_dir function automatically opens and closes a directory. Furthermore, it checks if the open was successful (which your code does not do). Finally, it excludes . and .. by default.
use File::Slurp qw(read_dir);
my @entries = read_dir($InDir);
Also, the rename doc mentions that File::Copy::move might be a more portable alternative.
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