The ignore list is user error, you mistakenly clicked on "Ignore" on the context menu that appears when clicking a player's name in chat instead of "Send tell", which is right above.
The hidden chat window thing is a bug by SOE, happens with all UIs. Deleting your uisettings.ini might help, not sure, but it's probably not worth it just for that. I'm recently seeing this on one of my chars as well, so I'll see if I can find a workaround for this problem.