I had this issue just after installing FF 2.0. I found an extension called flashblocker that basically blocks flash item from displaying unless you want them to. It puts a little circle the alternates between an F looking thing and a play button. Anyway. That fixed mine. Having the ad appear above the drop down menus really should be considered a bug and the appropriate people placed in a small room with only a slightly warped Yoko Ono 8 track for company.

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I'm not evil.
An evil person would do the things I think up.