Riggles - I have had a good look through the scene you sent me. The pauses are a function of building the ability to make meshes live or not (and visible or not) on the fly, without having to reload the scene. This has resulted in the need for every mesh to have it's own Geometry Group node pin, and your scene has 1500. So when you change a material, the plugin has to update the material and then see which of the 1500 meshes was using that material. That takes time.....
Whilst the ability for dynamically make meshes live or not is a great feature - I think the byproduct of slowing large scenes down so much is too much impact, so I will roll out that change in the next release.
Paul