Could very well be that wither the engine you are on is bugged, or that the specific terrain fails to generate correctly due to some obscure reason/dependancy or misconfiguration.
Make sure the scale of the landacape is 100x100 x/y.
Make sure the # of components makes sense and is divisible by 2.
Last thing to try would be to:
Export the heightmap and layer data for the landscape.
Then
Create a new level in which you create a new landscape, directly off the exported files.
Assuming the freshly created one has OK collision, then save it, and just replace the landscape in the original level with it.
If the exported files produce the same incorrect collision results, then the issue is far more likely to be whatver engine version you are on and whatver was bugged by the dev team.
Considering the changes and Nanite, its very possible that they introduced bugs… or that you have it set to process in nanite and its not working as intended.