Regarding setting, its seems any setting gives the same results. This was what happened with default settings:
http://i.imgur.com/6JUe9rd.jpg
Screen capture from kindle dx:
http://i.imgur.com/8OGZCGB.gif
Every page is the same size as the above screen capture, however just one page gives this size image:
http://i.imgur.com/Zu21Qto.gif
When i change settings from default to horizontal the same happens only one page uses the full screen of the kindle dx.
Also the size of the files after converting reduces significantly, for example from 13,495KB to 4,993KB.
Also regarding the single large image, when opening the comic from the kindle menu the first page shown is the little image which is page one. Then if i push the button on the kindle dx to go left there is the one big image: I have no idea maybe the conversion is not working.
My kindle dx is not jailbroken.