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For about a month, mouse clicks stopped working for me in Flash and Ubuntu, no matter the browser I use. Digging a bit, multiple solutions came up, so I will share them with you.

Solution 1 - this seems the best one but only works for i386:

1. Start a Terminal window and paste this:
cd /usr/lib/nspluginwrapper/i386/linux/
sudo mv npviewer.bin npviewer.bin.real
sudo mv npviewer.bin npviewer.bin.real
sudo gedit npviewer.bin

(one line at a time)

2. Add these two lines of text to the file
GDK_NATIVE_WINDOWS=true /usr/lib/nspluginwrapper/i386/linux/npviewer.bin.real "$@"

3. Press "Ctrl+x" to exit and save.

4. In the same terminal window, paste this:
sudo chmod 755 npviewer.bin

As seen here and here.

If you don't have /usr/lib/nspluginwrapper/i386/linux/, use the following method instead (This might work for 64bit, but I cannot test it):

Alternatively, for this solution, you could launch applications like so (simply edit the shortcut of any application you want - in which you are experiencing flash click issues with):

Obviously, replacing firefox with the application you want to run.

Solution 2: remove flashplugin-nonfree / flashplugin-installer and install from Adobe.

For an easy operation robau user @ubuntuforums.org has created a script for that. Simple copy the following code and paste it in an empty file, let's call it fix_flash.sh:

# Script  created by
# Romeo-Adrian Cioaba romeo.cioaba@spotonearth.com
# Jaša Bartelj jasa.bartelj@gmail.com

echo "Stopping any Firefox that might be running."
sudo killall -9 firefox

echo "Removing any other flash plugin previously installed."
sudo apt-get remove -y --purge flashplugin-nonfree gnash gnash-common mozilla-plugin-gnash swfdec-mozilla libflashsupport nspluginwrapper
sudo rm -f /usr/lib/mozilla/plugins/*flash*
sudo rm -f ~/.mozilla/plugins/*flash*
sudo rm -f /usr/lib/firefox/plugins/*flash*
sudo rm -f /usr/lib/firefox-addons/plugins/*flash*
sudo rm -rfd /usr/lib/nspluginwrapper

echo "Installing Flash Player 10."
sudo cd /tmp
sudo wget http://labs.adobe.com/downloads/flashplayer10.html
sudo wget `cat flashplayer10.html | egrep -o "http:.*"|cut -d\" -f1|grep linux-x86_64.so.tar.gz`
ARCHIVE=`ls libflashplayer-*.linux-x86_64.so.tar.gz`
echo "Version is $ARCHIVE."
sudo tar zxvf $ARCHIVE
sudo cp libflashplayer.so /usr/lib/mozilla/plugins/
echo "Linking the libraries so Firefox and apps built on XULRunner can find it."
sudo ln -sf /usr/lib/mozilla/plugins/libflashplayer.so /usr/lib/firefox-addons/plugins/
sudo ln -sf /usr/lib/mozilla/plugins/libflashplayer.so  /usr/lib/xulrunner-addons/plugins/
# now doing some cleaning up:
sudo rm -rf flashplayer10.html
sudo rm -rf libflashplayer.so
sudo rm -rf $ARCHIVE

Save the file, then use the terminal to navigate to where you saved it and run the following two commands:
sudo chmod 755 fix_flash.sh
sh fix_flash.sh

Solution 3: some users reported that the bug with mouse clicks not working in Flash & Ubuntu was fixed by either disabling Compiz or just by disabling the show desktop plugin in Compiz.

More info on this bug, HERE.

If you are using Ubuntu 9.10 Karmic Koala, see other things you can fix / tweak.