Well - if you not only want different IRC channels, but full MJ functionality on different clan servers - it gets complicated

because you have to use different MEGINJARDER.XML files depending on the account you log in. The plugin only accepts one database server definition (although there are some change requests according to this problem on the MJ developer board).
The basic solution is to copy the clan-dependent XML over the MEGINJARDER.XML each time you switch server=clan.
There are a few variations of how to do that, for instance manually in the Windows Explorer.
A more convenient way is to prepare batch files or a script with links you just have to double-click on your desktop before starting AC.
I will do that tomorrow and post the result here
Did you install MJ using the default path "C:\Program Files\Meginjarder" ?