Brown Dwarf Cloud Models There has been research that suggests that the changing brightness of Brown Dwarves are due to bands of Iron/Silicate clouds. Several models have been made that supports that hypothesis. My question is: Which part of the model are the actual clouds? Are the clouds the bright orange bits? Or are those bright areas “breaks” in the clouds and a view of the Brown Dwarf below.

5 MB animated GIF: Brown Dwarf Cloud Model
Initial research proved to be wrong as intuition does not match up with expectations. 

Anyway, the paper referenced by the OP seems to sum up the answer to the question pretty well:


  In  this  explanation,  the  dark  areas  of  our  map represent  thicker  clouds  that  obscure  deeper,  hotter  parts  of  the  atmosphere  and present a  higher-altitude (and  thus  colder) emissive  surface, whereas bright  regions correspond to holes in the upper cloud layers that provide a view of the hotter, deeper interior. 


Extract from A global cloud map of the nearest known brown dwarf

Initially I assumed that the metallic clouds would reflect radiation from the nearby star, however as it turns out the hot atmosphere is emitting infrared radiation which affects the brightness much more significantly.

More on Brown Dwarfs at here.