Sometimes the UI-File did also bug out.
But as it is now a XML-File you can easily edit it yourself. Look in your main EQ2 folder. There should be an CHAR_SERVER_uisettings.
XML file.
You can open it with any UTF-8 compatible editor. At the bottom should be a section including all you chat windows and tabs where also is listed which channels are shown. The game channels are hard to find out, as they are listed as one series of "0" or "1" bur below you will find the entries for your custom channels.
btw: The "new" uisettings file format is great for manual editing!