Just an idea.
I had this kind of problem (but not with Cloud Compare I think) working with georeferenced models.
3D softwares like meshlab for example cannot manage a point cloud or a mesh with terrestrial coordinates (very large numbers).
To deal with this problem you have to use the shift tool when you export your data with Agisoft.
For example if your X coordinates are 5000001, 5000001.4, 5000001.2, 5000006.1, etc...
You should use a X shift of 5000000 that translate you model.
Next you point would have X : 1, 1.4, 1.2, 6.1, etc...
Little numbers are more manageable by the 3D inspection software.
But it may be not the solution because I think Cloud Compare already manage terrestrial coordinates.