I have some scenes where the 3D alignment changes. For good viewing I need to have the R&L images properly aligned at various points. I have inserted keyframes for 3D alignment and used auto-alignment at each of these points. This changes the alignment for the whole scene rather than just at that keyframe. I have tried inserting multiple keyframes, but the alignment is constant across the entire scene and does not change with time. keyframes work fine for brightness and for size or positioning, but not for 3D alignment. If I do autoalignment and then insert a keyframe at that point, the alignment reverts to the original. I have also tried to vary the manual 3D alignment, but again it stays the same for the entire scene. If I break up a scene and align each part separately there will be jumps instead of smooth transitions.

Is there a secret hidden incantation needed to make 3D alignment work properly?