Unfortunately I'm not entirely sure when and how this happens, but there seem to be cases where, when you start the game with --use-ports=x,y,z, you will end up with a modified glestuser.ini which contains the values you passed as command line parameters. Ideally options you pass as command line parameters should act as one-time modifiers, becoming active temporarily but not permanently. In this case, however, permanent changes (i.e. editing glestuser.ini) seem to take place. To me, that's unexpected behaviour and my gut feeling is this will be so for most if not all other users, too.
It's also a less important issue unless you, you like, use a wrapper/start script to connect MegaGlest to given servers (and given ports) but also host yourself using the same installation/configuration files.
