Sorry about the late reply.
This might be because of the fact that the images themselves are little too bright (and the preprocessing step might not have taken care of this in bias correction). The EV quantification can be controlled by few parameters. Try playing around with the pmap_cut an clean_th values (see Doc pdf). You can go ahead and edit the WhyD_quant.m script (if you intend to explore more closely as to what's going on).
Please let me know if you have any more questions.