This is a issue because if you dont have certain layers available in unity, and you set a particle system to exclude 1 layer, then any layers missing from your project are also excluded. I have come across numerous world creators using the custom layers for world geometry, so any particle systems uploaded in a project without all the custom layers added just go through these. Please fix this in the SDK, all that would need to be changed is setting up all of the custom layers that you can use to something like "Custom X"