FUNimation got their masters for free from Toei because Gen Fukunaga had an uncle who was pretty up high in the Toei board it would seem. However Toei is...Toei. Their masters aren't the best (and the previews for the next episode lacked audio, unlike international releases) and so when FUNimation chose to remaster they simply through them in a automated machine where as the higher-grade masters Toei used for their DBOX release were cleaned up frame by frame (by a person, as opposed to a machine). FUNimation's 'remastered' sets also cropped off the top and bottom of the frames (which is something like 20% of the footage) and also washed out many colors (Season Two looking the most terrible, as I hear). Additionally, during the scenes where the footage is shaking (like during a power up or earthquake) lines DISSAPEAR. Completely. Additionally, detail is lost and sometimes so are faces in the background, as I understand it.
All-in-all many fans have refused to buy the FUNimation sets and have bought the DBOX or its singles.