I, too, am having a conflict with YARPP and the pagination nextpage feature in some of my single page posts. Using 3.0.7.
When I disable YARPP, the pagination works correctly.
If I keep YARPP enabled, when I MOVE the wp_link_pages function call ABOVE the_content, then the pagination works correctly (it displays above the content -- not where I would like it to be, at the bottom of the page, but at least it is displaying at the same time that YARPP is on the page). When I move the wp_link_pages function below the_content again, the pagination disappears.
My guess is that YARPP is exiting the loop, so anything else after YARPP in the site template that must also reside in the loop is getting gonged. This is on the Single Page loop, if that matters.
If this is truly the case, then where in the YARPP code can we place the wp_link_pages call so that the pagination occurs immediately before YARPP? My site is currently set to automatically include YARPP, so my next step would be to try adding YARPP manually instead. I would prefer not to have to do this, however, if a better option is available.