I haven’t really had any problems with clicks registering with Flash, not any more so than with OS X. The breakage I am experiencing with FF4b1 is much more severe than that, Flash objects simply do not render. I haven’t yet fired up the beta build from the terminal to see if there are any more informative messages there when hitting a page with a Flash widget.

There are only a couple of things I use that are Flash but sadly they are pretty important and there aren’t practical alternatives.