Before I explain, first two little things:
It's better to put these questions into the appropriate section, like Terragen 2 Discussion (support section is mostly for possible bugs or features, where the discussion sections is more about "how do I do/get this/that...?".
Secondly, there's plenty about this (actually everything) on the forums, so a search might help
Basically you need to check a few things if populations do not fit your terrain:
In the terrain-tab of your populator you can find two settings, the "sit on terrain" setting (which needs to be activated) and the "Planet" setting.
Make sure the name of the planet defined is the same as the name of the planet present in your network on which you've created your terrain.
By default the "sit on terrain" shader is "Compute Terrain". Check if this node indeed is the last "compute terrain" node in the node-network.
You may have deleted it or have replaced it with one with a different name.
If this all is correct and not the source of the problem then it's likely because you have (big) displacements after the last compute terrain.
Then you either need to add another compute terrain at the end and use that as "sit on terrain shader" or define the very last shader in your node network as the "sit on terrain shader".
After checking this at least 99% of the cases are solved.
I once made the mistake to enter a value in the Y-position in the object maker (NOT the populator node, but the object maker which actually contains the model you use to populate).
If you do so you offset your population by that given value.
So also make sure you didn't enter any value there, should be all 0 by default.
Hope this all helps.
Cheers,
Martin