I was probably a little to short in my explanation of what possibly is going wrong here. Recall that in Unix, if a process has a handle open to a file, and that file is deleted by another process, the file is not deallocated until the first process closes the handle to the file. I've never seen an explanation of what happens with directories, but it it's similar to files perhaps the following scenario applies:
Process #1 creates a directory. "mydir" The kernel is in process of creation but has not finished.
Process #2 tries to create the same directory, "mydir". It can't as the kernel is still busy with process #1
Process #2, being root, deletes the directory "mydir" and creates a new one with the same name.
Process #1 can't tell that its original directory "mydir" has been deleted, so continues to create the whole path to the file it needs to create.
Process #1 completes. Its copy of the original "mydir" directory is deallocated along with all the files that depend on that directory.
Seems plausible to me.