Hi, @roldyclark.
I recommend checking that the WordPress user you’re logged in as is either an Administrator or a role with the ‘unfiltered_html’ capability.
For non-admin users, you can use a plugin such as User Role Editor to check capabilities for each role. (After installing that plugin, visit Users → User Role Editor, then select the role, such as “Editor”, and make sure “unfiltered_html” is ticked. Note that this will change the capability for all user with that role.)
The “Execute PHP on this hook” option in Genesis Simple Hooks will only appear if you have the “unfiltered_html” capability. It sounds like installing and uninstalling the Unfiltered MU plugin you mention has removed the capability for your user.