We need more specific information. Here are a few questions:
I created a new one-click deployment package. I changed the RU server to my servers FQDN.
The settings did not carry through. It set the FQDN & port back to the default, ignoring my settings. It did keep the password I assigned.
Was it an upgrade of a remote Host, or were you installing a new Host on a machine without any previous Host installations?
I'm asking that because the outcome may depend on what you specify in Step 4 of the configuration process.
MSI package carried the options through.
I guess you mean the Standard MSI package (first option in the MSI Configurator). Did you use exactly same settings of the MSI Confiurator when creating both packages? Namely the settings in Step 4.