When you specify a directory where a map will be mounted in auto.master, 
if it does not exist, autofs will create it upon startup and remove the 
directory when it shuts down.  However, if the directory already exists, 
autofs will still remove it when you shut down.  I've attached a patch 
to autofs-4.1.3 which will prevent autofs from removing previously 
exisiting directories.

If you have any questions, let me know!

Thanks,
Chris