@Ofer Wald,
Can you elaborate on this a bit? Some of the information is over my head, so I can't tell if what you're talking about is related to the problem I'm observing.
The plugin seems to be injecting multiple instances of the WP permalink rewrite into the .htaccess which then apparently affects the pages on my site - not the posts, the pages.
While I seem to have something in my .htaccess (I'm assuming cache related) that is affecting visibility of pages in varying ways, I've now seen the problem go from affecting only certain pages I'd edited to all of them when Yoast's plugin in activated. In both instances, I've had to go look at .htaccess and I see the multiple injections of the rewrite, some of which are garbled in that they are only the #BEGIN WORDPRESS #END WORDPRESS. When I clean up the file, the problem reverts to the few pages.