You are probably experiencing an issue with ownership. If you copied the files using Windows File Manager, the copied files do not have the same owner:group as your cygwin setup.
In your cygwin session (just after you open it), execute the command 'ls -l', you should see something like this:
total 38
drwx------+ 1 owner mkgroup 0 Oct 17 10:41 .
drwx------+ 1 owner mkgroup 0 Dec 8 2010 ..
-rwx------+ 1 owner mkgroup 18780 Oct 17 14:06 .bash_history
-rwx------+ 1 owner mkgroup 1150 Oct 25 2010 .bash_profile
-rwx------+ 1 owner mkgroup 4047 Oct 17 10:45 .bashrc
-rwx------+ 1 owner mkgroup 1461 Oct 25 2010 .inputrc
-rw-------+ 1 owner mkgroup 54 May 24 15:55 .lesshst
-rw-r--r--+ 1 owner mkgroup 112 May 9 10:17 .minttyrc
drwx------+ 1 owner mkgroup 0 Dec 8 2010 .ssh
The third column shows the owner id (I changed the actual owner id from my real one to 'owner') and the fourth shows the group.
Now execute the command 'chown -R owner:mkgroup *' (substitute the actual owner value you got from the previous command).
Then execute 'chmod -R a+r,a+w *'. This will make sure that everything is writable.
Then go to your project directory and do a clean and build.
You will need to do the chown command in your project directories any time you use Windows File Manager to copy files into it.
Cheers,
Ancient Lady
AGK Community Tester