I have a folder /cygwin/d/myfolder/ And everytime I save files there, from cygwin if i do an ls -la I see that the files are given permission 000. That actually causes me qu
Check to make sure that your umask is set correctly with the umask command. If your umask is say 0777 that subtracts from the permissions of new files and will end up with 000 permissions. There's probably several other possibilities to consider beyond that.
If your id is not set up correctly in /etc/passwd and /etc/group that can also cause ls to show unexpected results. Check the permissions of the folder. Also check the Windows permissions with the getfacl command. Maybe also check the mount command.