For some reason, I noticed that sometimes the surfaces generated by the Sandbox tool have very weird normals. I don't know why, and I don't think I can do anything about it from Skatter.
As the grass presets are configured to have the pointing direction halfway between the up axis and the surface normal, your components end up rotated sideways.
The workaround I found is to explode the group generated by Sandbox, then group the geometry again, and then start Skattering.
Either way, please send me the file so I can take a look at it : email@example.com
Rombout, you are seeing a different issue, I replied to you in your own thread.