Apparently Cygwin defaults to using POSIX permissions. Some files generated by Windows apps set ACLs that are then interpreted incorrectly by Cygwin.
The only work-around I have found is to change the way Cygwin mounts to the filesystem to ignore ACLs. I modified the /etc/fstab in the Cygwin root to uncomment the following line and add 'noacl':
none /cygdrive cygdrive binary,noacl,posix=0,user 0 0I had to close down all of my Cygwin processes and relaunch them to fix the problem.