Actually, I know of at least one post house that has fully licensed copies of Sapphire and Shake which was running into the same problem. GenArts was blaming Apple, and Apple was blaming GenArts (as usual... 
)
What I was eventually told, was that certain versions of Sapphire did this with certain versions of Shake, and that the only sure fix (aside from looking over the render and asking Shake to re-render specific frames and/or specific series of frames), was to make sure you are using the very latest version of the plug-in with the very latest version of Shake.
Sorry I can't be more specific- they eventually told me which version of Sapphire worked perfectly with which version of Shake, but I'll be damned if I can remember what was what- anyhow, I know that the latest version of both worked well with each other and eliminated the "black bars" issue.