After selecting/deselecting to add-ons you want in the RTB mod manager, you have to restart Blockland before the changes are copied to the Start Game screen.In-game RTB server settings are not saved the next time you start a server.
Make sure you're using the latest version of RTB because I fixed the server settings problems ages ago.
I'm pretty sure it automatically updates.
...What version does it say? Latest I believe is 4.04
To further clarify, the only problem with the RTB server settings not saving that I'm finding is the welcome message.