I forgot where I found this workaround, it worked on Karmic 64bits:
Open terminal and enter:
gksudo gedit /usr/lib/nspluginwrapper/i386/linux/npviewer

then add: export GDK_NATIVE_WINDOWS=1 before the last line of text

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[READ DESCRIPTION] Flash is not recognizing mouse clicks in multiple situations
https://bugs.launchpad.net/bugs/410407
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