I’ve just had the same problem, took me one hour to reinstall the whole thing and figure out what is happening. Turns out, I’ve had set my posts not to be older than 12 months in YARPP settings. Therefore some of the manually picked ones were not displayed. The moment I’ve turned this setting off, all my manually selected posts were displayed.
Btw., this note could be a part of the settings page or WRI plugin, just like there is a warning to turn of automatic display of related posts in YARPP settings.
Hope it helps