As I said in chat last night, I've had none of those problems.
What I did is right click on my main chat window, and select Add New Tab. I did this several times. I then went to the Chat Options for each tab and set the tab name and which channels/info I wanted on each tab. I then repeated the process for a 2nd chat window, so my UI looks like this:
I've not experienced any chat clearing or other problems; it works flawlessly for me, and I've not heard anything bad about them from my guildmates. If you are experiencing strange errors like this, then I'd recommend deleting your eq2_recent.ini and your character's specific ui ini files, and starting your UI layout over from scratch.