I've tracked bug #1 down to
my commit for fixing the cosmetic disappearing icons when reordering files in Book Browser (Linux/Windows only).
Reverting the change alleviates the issue of reordering multiple (but non-contiguous) files in Book Browser. If I can't find a solution that will accommodate both, I'll revert the cosmetic fix and some people will have to deal with disappearing icons after drag and drop operations.
I have some ideas and leads to follow up on, so hopefully I can find a unifying fix.