Hi
No, there isn't continuous collision detection in jinngine, What size does the boxes have? What is the timestep size and is the initial velocities zero? Anyway, it is a common artefact. But from what you describe, it sounds like the boxes are initially at rest (in contact). So in principle, you wouldn't benefit from ccd in that case.
In case you're not already using it, try the "geometry_rework" branch, that has the newest changes.
Morten