The last time I saw a problem like this was with water, but the latest update fixed that, exposing the seed value, allowing it to be fixed. Populations on the other hand have had the seed value visible as long as I can remember, although for some reason it appears to be broken. I'm not sure if I've rendered an animation with objects using the latest update prior to this, so at the moment I'm wondering if something broke with the update?
... Tried reducing the movement increment of the population and it appears that the placement is linked to the population's location. Thinking back now, I don't recall rendering an animation with a mobile population. I had set them up for performance testing of the populator, but may have only rendered animations with mobile population density shaders.
This is potentially a bad thing because you need to move the populations with the camera in an animation to maximise performance. You can mask the distribution of a population to a small area to reduce the number of objects but the time the populator takes to calculate a population seems to be solely dependent on the area of the population, not the number of objects. To maximise performance then, you need to minimse the area of the population to only cover the area in which you require objects to be rendered, which requires moving it with the camera.
If the coordinates of the population of the used to calculate the placement of objects this might be better with a random, constant vector, specified with the seed value (or just a fixed one? ... tweaking the seed should provide enough control over variation?)
