darcyle2, you did probably change something in the windowsettings and made the window or it's titlebar only visible on mouseover. Change it back there, no XML editing necessary.
aigor, so I guess you checked that your XML has entries and is correctly formatted (or you tried with the XML provided by me)? I'll have a look at the window again, but I currently don't see why the list could be invisble...
silent1, hmm, the [x] is supposed to be there. Maybe it ran away when I wasn't looking, I'll have a look and will try to hunt it down.
Limp, I'm sorry, but I do not support EQ2Map, this is the thread for ProfitUI here.
And I am also not sure whether I understand your problem, but you can set waypoints by typing /way <loc>. Best ask the EQ2Map guys though if it's something else you are wondering about.
And thanks everybody for the props, always good to hear.