When you start a render, the populator is supposed to automatically repopulate if it thinks something in the scene has changed which might affect the population. Typically these are the density shader, the terrain shader and the planet connected to the poulation. There was a bug in 126.96.36.199 (and some earlier versions) which caused it to ignore most changes, therefore it "forgot to repopulate". More precisely, it would repopulate for changes that were intended not to require repopulation (such as Preview mode, bounding box settings and things like that), but if you make a few different changes in the scene you might not realise it's doing anything wrong. You might think it was working properly most of the time.
I've fixed that for 188.8.131.52, so it will now repopulate in the cases where it's designed to, and not repopulate when it recognises that the only changes are harmless. That's the theory, but in practice I know that it may be a little over-zealous in some cases. Sometimes seemingly innocuous changes to the scene will result in a repopulation even though we, as humans, know that it doesn't need to.
In your case, in your new scene perhaps there are more things connected to your population, or you made different kinds of changes that resulted in repopulation.
This problem has been raised by our alpha testers and I plan to improve this. One suggestion is to make population a manual process only - you would always have to tell Terragen to repopulate, unless you've just loaded a project. One problem with this idea is that your population might look different when you reload the project compared to when you last rendered an image, if you forgot to repopulate when there was a change. I think that Vue avoids this discrepancy by storing all instances in the scene file, but we don't do that yet. It hugely increases the size of the scene file. When we introduce population caching in future, this would solve the discrepancy but greatly increase the size of the project file. Another idea is to make the populator much more careful and intelligent about what changes require repopulation.