Hey aimeX,

I have experienced and been notified about this earlier before where it came out that servers with no players will not be shown in the masterlist.
You may consider setting up a bot mod which makes the server always have at least one player (bot) and whenever a real player connects, the bot disconnects.
Please try this out and tell me if the server is listed in the master server list when a player is online.

/JoNny