OK great - having looked for just a few minutes:
1. The way the box falls, it doesn't look like CCD is enabled - are you sure it's enabled in the filter shader as well as the scene and dynamic actor (I can see the flag is these two)? However, this is not the cause of the problem.
2. Your box looks like it's about 50 units across. The contactOffset value is 0.02 which is tiny, in proportion. I'd suggest setting contactOffset to 1. But I don't think this will solve the problem.
3. The scene is reporting gravity as (0,0,0) (and the object has eDISABLE_GRAVITY) - is that right? So you're applying gravity manually? I don't see why you shouldn't - a constant force shouldn't cause penetration problems... but maybe it is.
4. PVD doesn't report the tolerancesScale length/mass values - but it does say the "normal" speed is 10 units/s. When your box falls it his the ground at about 909 units/s
1. Disable CCD for the moment - it hasn't been reliable in the past (though is probably fine now)
2. Make sure the PxTolerancesScale is set correctly
3. If that doesn't work, see whether it's due to disabling gravity and applying the gravitational force manually (if this is it, it sounds like a PhysX bug).