FS-UAE Launcher divides the FS-UAE options into two categories, you could call them "configuration options" and "settings". The settings are generally common for all configurations (but can be manually overriden in configurations, there are UI for this). The fullscreen option is such a "setting", but it is not intentional that the option is deleted from the configuration files! -So I'll look into that.
One thing you can do is to create the file Host.fs-uae in Configurations:
Code:
[fs-uae]
fullscreen = 1
This will will be used to read common defaults for FS-UAE (but will be ignored by the Launcher). This way, you don't have to store fullscreen = 1 in all your configuration files
