i too am suffering from this bug. No mouse clicks in Flash. The R-click 
workaround did help. Switching to metacity also helped. However this bug is 
being experienced by people who do not use Compiz. I ran about:plugins in 
Firefox. I noticed Firefox was not using the normal 64 bit plugin i had 
installed, it was using.
npwrapper.libflashplayer.so
While helping someone in a support channel I did install the 
'ubuntu-restricted-extras' package (I am assuming where the 32 bit flash plugin 
came from).

duanedes...@duanedesign-laptop:~$ locate libflashplayer.so
/home/duanedesign/.mozilla/plugins/libflashplayer.so
/usr/share/ubufox/plugins/npwrapper.libflashplayer.so

You can see it located my 64 bit plugin in my home directory and the 
npwrapper.libflashplayer.so.
I  uninstalled 'flashplugin-installer' and 'nspluginwrapper'.

I launched Firefox put about:plugins in the address bar and got:
libflashplayer.so
Good I thought. So I proceeded to YouTube, which worked great, and was able to 
use all the Flash buttons. However visiting  Gmail crashes the browser 
instantly. No turning gray, it just disappears. 

So fixed one problem, have a new one. Well same problem, different
symptom  :)

See this blog post. Describes the problem well and has a solution (which
unfortunately did not work for me). He got to the point I am at and
installed the package 'libadns1'. This worked for him

He compared the output of ldd libflashplayer.so while running 64bit
Firefox on Karmic and in a Jaunty chroot (ran fine on the latter). He
noticed one extra library was showing up in the chroot, libresolv.so.2
which prompted him to install 'libadns1'. Also worth a note he was
running Sawfish and does not use Compiz.

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