I moved this to the AIR forums. I'm actually surprised that we throw a prompt in the context of AIR, but I guess that you could theoretically load a third-party SWF into a WebView in your AIR app, and you'd want the end-user to be able to see and control that behavior.
The reason that clicks get ignored is because we're checking to ensure that the dialog is not obscured (at least in Flash), and we sample pixels from the screen (in modern browsers with hardware compositing, there's more complexity) and compare them to a buffer of what we *think* we're rendering, in order to evaluate whether or not we're on top. Things moving around the edges of the settings window like video and gameplay will often confuse it, but we may run into platform-specific issues that cause these checks to fail. Because Flash is running as plug-in inside of the browser (and in modern browsers, outside the host process and restrictively sandboxed) there's really just no better way to do resilient clickjacking protection in a way that minimizes false-positives.
Because of the privacy implications, we can't really kill off the dialog. In Flash, I'd love to see it moved into the browser chrome, but it would require support from every browser vendor, and it's not going to happen at this point.
The easiest thing to do is probably to just avoid having it ever pop in the first place. Off the top of my head, I'm thinking that EncryptedLocalStore() is probably a better choice for local storage in AIR, just because you're not carrying around that Flash legacy. I don't do enough AIR development to remember off the top of my head whether or not ELS throws it's own prompt, but my guess is that it doesn't, since you can't call it from Flash...