Is the Problem SQLite 3 or Cuberite?
It looks like the problem is with Cuberite, but we're not sure why. We also can't reproduce this behavior, so there is no way for us to see what is the bottleneck.
Could we implement Callbacks like them in cNetwork in cuberite? Then it could run in a own thread?
Just a tought
Just a silly question: Are you, by any chance, running Cuberite from a network-mapped storage? Or a slow SD card, or something equivalent that would make disk IO slow. That could explain it.