Hi there,
The best solution to this would be to install Ubuntu normally, and then add MATE after with this command:
sudo apt install mate-desktop-environment-extras
The Ubuntu-MATE installer may be configured differently than the standard Ubuntu Unity installer, and Unity is integrated into Ubuntu in funny ways, so we recommend having both, and just using MATE, rather than using the Ubuntu-MATE installer.
We may have more information here: http://support.system76.com/articles/desktop-environment/
But please reach out to our support team if you continue to run into issues. We’d love to troubleshoot with you to get this resolved.
Thanks!