If I have multi-player set up and I uncheck multi-player on the screen that is used to launch flightgear and then close fgrun the multi-player settings will be gone the next time I run fgrun. So at that point I have to go through the process of setting up the multi-player network settings again if I want to use this feature. These network settings should be persistent even if the user has disabled this feature.
Also on a related note perhaps you could add a default button to the Advance Options -> Network dialog that would automatically set this up for the standard fg multi-player servers. Then all a user would have to do is press the default button and enter a call sign. This would make this much easier for users to setup.