In Ubuntu 9.10 amd64 I was unable to click flash videos. I believe this is a confirmed bug. You can fix it by doing the following:

Alt + F2
gksudo gedit /usr/lib/nspluginwrapper/i386/linux/npviewer
add the following line BEFORE the last line of text
export GDK_NATIVE_WINDOWS=1

Save and exit the file.
Restart your browser.

original info from here.

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