As far as i know if the channel is registered as you say, the modes should stick. Perhaps another user is removing it on you while you are gone? You may look into mode lock (Usually /chanserv set #channel mlock or /chanserv help set mlock for help). You might be abel to set soemthing such as:
/chanserv set #channel mlock +b *!*@*aol.com
Where a ban would not be able to be removed, nor another one place. If you know its not another user, you may want to find out the IRC software the server uses and look into how it runs. This can easily be done by looking in the status window while your connecting. At the top, you should see some form of greating such as "Welcome to <network>" and below it listing soemthing such as:
Your host is <server>, running version Unreal3.2-beta17
If all else fails, try joining #help or #oper. Those are usually designated channel for the operators of a network. You can try asking them why your ban would not stay.