HTM is at its core a temporal memory system, so yes, every data is processed one row at a time. Synaptic weights and connections may be mutated at each time step.
Are you saying that the input has a 2D topology? If so, you must create a 2D topology in the SP as well. Watch this video first: HTM School Episode 10: Topology
It is hard to tell what your graphs are saying without understanding more about the semantics of the data. 400x200 is a pretty large input vector. How many minicolumns are you using?