You shouldn't have to manually set a bookmark. When I've used the stock reader I just "left" what I was reading. I returned to it using the "continue reading" icon. It returned to what I was reading (last page read). If the icon didn't work, selecting the book again did.
Try rebooting. Sometimes you just have to.
Edit: Most of my content is sideloaded. The only things that aren't are the B&N freebies.
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