If your flashplugin only recognizes the very first mouse click and then seems to ignore the mouse completely, just click somewhere outside the area where the flash script is (e.g. on the webpage background) and then flash will recognize the next click.
Some more promising solutions are these:
ubuntugeek.com: edit the file
/usr/lib/nspluginwrapper/i386/linux/npviewer and add the following line just before the last one:
The complete file should now look somewhat like this:
#!/bin/sh TARGET_OS=linux TARGET_ARCH=i386 export GDK_NATIVE_WINDOWS=1 . /usr/lib/nspluginwrapper/noarch/npviewer