Footprints are stored in the pcb_new file where as 3d models are not.
You get problems if the used lib changes somehow.
If these projects use the official libs and they have been created a while ago there is a high chance that the files have been renamed in the meantime. There is a much higher chance that the scaling of 3d models has changed. (Until last year the scaling of 3d models was made within kicad, now we expect the 3d models to be scaled correctly.)
If the projects use their own footprint libs, they should also have 3d model libs. In this case you need to copy the 3d files to the location where they are expected. (see below)
How to find out what's wrong?
For each component that does not show up in the 3d viewer do the following:
open the properties dialog and switch to the 3d settings tap.
What does this say? Look with a file browser in the expected location. Is it there? Can you see a pattern for what is there and what is not there? (Example missing lib, renamed lib, ...)
How to fix it?
Either make sure all footprints point to the current 3d model.
- For old projects not as easy as one might think. (updating the footprint from the lib via the change footprint feature does not always update 3d settings) This might mean you need to change the 3d settings by hand.
Or create the expected 3d model lib structure
- If you know with what release the project has been made, you can checkout the same version of the lib. (The github repo is tagged for each release.)