I have the same problem BUT only in Chrome. I only use Chrome for browsing the site and those panels disappearing don't affect that browsing, posting, etc. It sounds like when you want to play you hit that Play Now button (if you can see it) and starting your game this way is inviting all of the main site bugs into the game. This is not good.
A very simple way to do this is get another browser for the game and just have it for the game, nothing else. You set it up to open directly in the game client and avoid all the main site stuff. Andyson would call it a hoop you have to jump through to play the game but it's too simple to ignore and hugely beneficial to playing the game.
This doesn't excuse WGT for their (or Flash's) incompetence in fixing it but it's better than waiting for a fix. :-)