Cygwin and File Permissions

I was running into a problem while setting up command line scripting of the Altera tools. Some files generated by SOPC Builder would have permissions of 000 in Cygwin so quartus_map would fail because it couldn't open those files in read mode. 

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 0 

 I had to close down all of my Cygwin processes and relaunch them to fix the problem.