My (very limited) impression is that the days when the ATIS gets the cloudbase wrong are sometimes those when there are lots of gaps in the clouds, or when the cloudbase is a bit lumpy. Perhaps the problem is that the laser doesn't hit the bottom of the main layer of cloud, but passes through to the layer above.
Again just my assumption... I was interested in Genghis rule of thumb that you can guess the cloudbase by whether or not you can see texture in the clouds. Presumably it means there's a definite 'feature' size to them. I'd always imagined bigger clouds as looking much like smaller clouds, but bigger. I'll have to look more closely.