Hello, for me I found a nice workaround. It looks like the <<show
desktop>> plugin causes the bug. I use compiz now and have this plugin
disabled. Enabling changes appearence of the plugin regulators and
disables mouseclicks. Disabling the plugin changes appearance back in
flash and mouseclicks work again.

I am using a intel quad core amd64 machine with crossfire ati cards on
karmic.

Hope this helps someone.

Greetings Johannes

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flash does not recognise mouse clicks
https://bugs.launchpad.net/bugs/410407
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