What was the material assigned to the Sphere?
We had reports of problems with Brazil r/s 2 (which we fixed in v2.0.2), and a report about finalRender materials rendering transparent.
Krakatoa has to evaluate the material on the matte object since it respects the opacity mapping (fully opaque pixels will show particles through).
If you can reproduce the problem and let us know which material it was or what maps it had, we will look into fixing this in the current build. Of course, we cannot do much for 1.6 at this point.