I have found that when I switched from AAMEE 3.0 beta to 3.1, I started receiving error messages like these. They come up when I double click the PKG straight from AAMEE. I believe the problem relates to permissions on the update files that AAMEE retrieves. I run the following command and it generally allows the package to install "chmod -R 755 /path/to/AAMEE/generated.pkg" (obviously without the quotes). This gives every file inside the package the read and execute permissions the installer needs.
Edit: Thinking about it, it could just be the updates and have nothing to do with the difference between 3.0 beta and 3.1. There weren't any updates to install back then.