Your problem description doesn't reflect my experience:

c:\test>dir /b fred
File Not Found

c:\test>perl -E"mkdir 'fred' or die $!; mkdir 'fred/bill' or die $!"

c:\test>dir /b fred
bill

c:\test>dir /b fred\*
bill
[download]

The only thing that I can see that might change the above, is if the code you are using has set the umask?