I don't know but I'm wondering if you're running any simulations in the animation. If you are, it could be that you jumped to a frame in the timeline when you took the single pictures. If you do that, the simulation doesn't calculate all the frames before it. If you do a batch render, the simulation calculates every frame. This would matter if, for example, you have fluid clouds that partially block your light source...

I assume you didn't change the quality from draft to production?

Except for those 2 possibilities, I have no idea.. sorry