Physics objects are touchy about being moved with the set position action. It confuses the physics engine when things suddenly teleport.
Anyways, I haven't done it in a bit but you should be able to keep the velocity by:
1. save the the velocities to variables.
2. move the object.
3. wait a tick and set the velocities from the variables.
Or just use the chipmunk behavior, it doesn't have that quirk. You can just simply move stuff without issue. Anyways either of those should fix the relocation issue.
The objects raining from the sky is probably from them being launched there from off screen overlapping objects.