Flags are stored on the server, not the client. Are you getting the same slot when you re-join the server?
Also,
flags for each user are cleared when the client is authorized (client_authorized) and when they are put in the server (client_putinserver).
How are you being authenticated in those servers? Are you using SteamID? Also, have you verified with an actual Steam server (i.e. not ReHLDS)?