I cannot get rid of the quit notifications in my status window. I have checked Events and everything is set to display only In Channel, so I am not sure why this is happening...though we had a storm the night before, but everything else seems to be working.

I've had this before, assumed it was related to auditorium mode. I think the server gets in a state where it sends you quit messages that you never received join messages for.

You can fix this sort of nicklist desync by typing the command /names #channel

If this is a bug that can be reproduced, please post a step-by-step guide in how to make it happen.