the flash is viewable but not active... hover your mouse over it, do you see the box around it? and let it stay for a while and you'll see the tag that says, "click to activate"
OK, now I see what you mean, and I agree it's annoying. And, apparently, it is the result of recent Windows Updates. I don't knoe what you can do about it; re-designing the site would be a huge task, no doubt.
However, I believe your description of it is erroneous. It's an ActiveX issue, not a Flash issue. Or, it's how you use Flash. That message, "Click to activate ...", does not appear on every occurrence of Flash when view various sites. It appears to be the use of Flash in menus or certain other uses that triggers the message.