Yeah I've been experiencing this issue from the beginning... Same as you, I have tried on tens of clean installs.
I am so overwhelmed trying to solve this,

but no way... Babiato team does a great job here, but I think the issue comes up as the theme builder tries to make a cloud connection to thrive servers to replace the sections... Since it can't, so it doesn't replace the sections..
This is error seen on dev tool's console...
I have tried two different cases.
- By using original thrive membership
- By using an agency licence
Replacing sections only worked at option 1, thrive membership. I'd be great to replace sections, because I think it adds value to your inspiration during design. But I don't think it looks possible. If there is somebody who could succeed to replace sections, he'd be sorely appreciated!
Maybe Babiato team could find a workaround at some point.. I hope