Ok, so I think I've figured it out.
Don't use the Animation codec when saving your movie capture through Snapz. Instead, use the h264 codec at 30fps (frame reordering box not checked). Keyframe every 500 frames, choose Multi-pass encoding mode, and drag the Compressor quality to Best.
The sequence settings I used in FCP are shown in the attached picture. My export settings out of FCP are shown here as well. This may not be someone's ideal method, but it worked for me and I'm happy.....for now!