What is the full model or product number of the desktop you are upgrading? I take it you are upgrading from Windows 7 to Windows 8. Is that correct?
Are you getting the same warning about the Microsoft Security Essentials each time? If so, it sounds like it isn't uninstalling properly. Try using the FixIt found here to review the list of programs it detects. If it detects Microsoft Security Essentials, use the FixIt to uninstall it.