Not sure which instructions you followed but I’d suggest this post on how to setup Duplicati as a service in Windows. I’ve also posted to that thread here regarding some of the side effects of moving to a service based install. Make sure all of your shortcuts to Duplicati have the --no-hosted-server switch.
Off the top if sounds like your Duplicati-server.sqlite database didn’t get migrated to the new service folder, so your jobs only exist in the tray server and only launch when the tray icon gets launched.
If you reboot and go directly to http://localhost/ngax/index.html (Don’t click any Duplicati icons) do you get a seemingly “new” copy of Duplicati with none of your previous settings? If so that is the server copy of Duplicati that’s running it just has no config. The above mentioned link should fix things up, if not ask away.