+1 to Emma's suggestion ...
"I missed the view I had set, the conditional field plugin and the local mail test and static page plugins"
Sounds like Installertron didn't do
"Next, copy across your config.php, any custom plugins, and your .htaccess file if you created one (check that custom plugins are the correct version for your new Moodle first) ... "
as described in https://docs.moodle.org/39/en/Upgrading
So how could that be a bug in 3.9?
Applications like Installertron are commercial and provided by hosting. Installertron isn't open source so no one can inspect what it does to determine if it is correct or not.