My guess is that the Box2D engine is just not very good. In the first test, for example, if you change the velocity to -50.0001, the balls start to bounce. There are probably some "magic numbers" used in the engine code, which may explain these anomalies..
I made a quick test in C2 with Chipmunk physics and it seems to be much more accurate. Unfortunately, as far as I know, this plugin has not been ported for C3.