I've renamed my /usr/lib/nspluginwrapper/i386/linux/npviewer.bin to npviewer.bin.real, and created an executable script in place of npviewer.bin with the following contents:
GDK_NATIVE_WINDOWS=true /usr/lib/nspluginwrapper/i386/linux/npviewer.bin.real $*
This completely fixes the clicking problem within Flash for me. So far I've had to implement a hack like this for Java, Mono and Flash. It hasn't presented that much of a problem, but to have three major platforms malfunctioning like this just looks bad. I really hope the GDK_NATIVE_WINDOWS work-around makes it into the Flash, Mono and Java packages soon - obviously the upstreams need to fix the bugs with the way they use GDK, but I wouldn't want to hold my breath waiting.