One of the things that can cause that is not having the right permissions/ownership of files/directories.
Try this using the cygwin window:
umask 0000
cd /cygdrive/c/Android
chown -R <winusername>:mkgroup *
chmod -R a+r,a+w *
The first command makes sure that all permissions are allowed on all files/directories created by processes in the cygwin session. It only applies to the current session, so should be executed as the first command whenever you open a cygwin window.
The second command changes your current directory to the top of your Android setup.
The third command makes sure that the ownership of all the files and directories is the same and that it is you, the Windows user. Make sure to substitute your Windows user name for <winusername>.
The fourth command makes sure that all the files and directories are readable and writable by everyone.
The combination just might get rid of the command.
I assume that you are doing Tier 2 since you talk about the template. Did you download the template from the TGC 'Your Products' download page? If not, try doing so and building it to make sure your setup works.
Are you working with v1076? And was your Android setup created with that version?
Cheers,
Ancient Lady
AGK Community Tester