If you run into permissions problems or your directories' security ACLs are populated by some unwanted groups/users, you need to make sure that:
- File ../etc/fstab exists with at least the content below (with Unix line endings even if the file has only one line!):
none /cygdrive cygdrive binary,posix=0,user,noacl 0 0
That will instruct Cygwin not to touch permissions.