We're also experiencing this still - mostly on Firefox 18, with Flash 11.5.502.149, OpenTok JS library v1.1.2. Additionally, when a (non-Retina) external display is connected, the problem doesn't occur - even on the Retina display portion of the desktop, but when it's just the Retina panel with nothing external connected it goes back to being unclickable.
This is a major blocker for us. None of the usual tricks (resizing the window, global settings windows, et al) work.
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