Screenshots of what you're doing.

In this case I checked "solid" which perfectly clips the misc_model. But this should only be done with complex models or models which need a high detailed clipping. Otherwise you should use a brush covered with the "common/weapclip" texture. (-> e.g. boxes, lamps, ...) Additionally I checked "force_meta" to force grid-lightmapping which looks way better than vertex lighted (but also takes more time to compile the map).

You know that autoclipping creates couple of brushes per tris in model? And it's destroys performance?

So for example - compare clipping a box (one clip brush for it) or auto clip (count triangles and do the math).

Or Xontotic has some magic q3map2 version which deals with this problem O_O