I know this has been reported before, so I don't know if it is a regression or something that hasn't been fixed... ahem. [;)]
After closing a PBB project, the closed project is shifted ~10 projects in the list. When you close a project, the project should still be visible!
If I remember correctly, the devs had difficulties reproducing this issue. It helps if you have more than a few personal books. [;)] FWIW - I have more than 100.