There is a simple solution to the combat chat frames disappearing. Untick the auto join guild box in advanced ui options.
This is what is causing it. Blizzard know about the problem and are supposedly going to fix it next patch.
I get the disappearing box problem regardless of whether this button is ticked or not. It usually happens after zoning. It's not a SimpleCombatLog problem though as it still happens with NurfedCombatLog, or with most of my addons disabled :(