arnold and J:
I noticed the same issue with the flipping of dimensions. I fixed this by transposing the count ouput parameter (count') before using it in scatter or pcolor or any other plotting function. Hope this helps :)
i was looking for 2 entropy implementations that give the same answere. And i found it, but guess what? its because they are the same code.
the jentropy used in this submission is the same as the entropy file here http://www.mathworks.com/matlabcentral/fileexchange/12857-entropy.