There has to be something common between those rooms on that server, and something that doesn't occur with other rooms.
Can you confirm this behavior with no scripts running?
Also please report back the following information:
1) The return from //echo -a OS: $os Version: $version Scripts: $script(0) DLLs: $dll(0) MD5: $md5($mircexe,2)
2) The name of the server that you are having difficulties with.
3) A few of the channel names that you are having difficulties with.