Thanks "missing files" is an information.

There are any possibilities, it could be your filesystem, it could be a perl bug, it could be a stupid race condition.

For instance I had very confusing results in the tests of my first reply, deleting the opened directory before reading the files produced different results in consecutive runs... maybe I was to tired to nail down the problem.

Anyway running your code now, with all messages (Fatals, Warnings and $!) catched and logged should hopefully give you a hint for suspicious signals.