Deactivate all your filters (detail, patches, etc) and deselect everything (press ESC a few times). Then press ALT+2 to filter entities from view. Press I (invert selection) to select the entire map. Press ALT+2 again to unfilter entitites, then press I again. Viola, all your entities are selected.
I always used the latest download of Q3Map2 for doing mine. I am not sure what version it was, but I am fairly sure it was later than the one that came with 1.3.12. I downloaded it from the shaderlab web site.