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.

NB! You may experience very slow transfer rates and/or building the file list may take long time. You can remove /etc/fstab and use the option --no-perms  option instead. The problem can also be related to real-time anti-virus scanning. Consider file/folder exclusion if possible.

More information:

The Cygwin Mount Table

The cygdrive path prefix