We faced the same problem and couldn't find a solution, so we used an older version of the deeplink module which contains its deeplink login page.
Yesterday we came to the conclusion that the newer versions of the deeplink module seem to fail for us using the out of the box configuration. Since 6.1.x the default behaviour is that you are redirected to the login.html in your theme folder rather then that the login.html in the resources folder is rendered. While this change itself seems very nice, i mean no longer do you have to style 2 login pages, who wouldn't want that right :) However what does bother me is the fact that the custom login page in the deeplink module seemed to have a functionality that redirected users to the deeplink again after they logged in. Basically it remembered the original deeplink during the login attempt so that they user is still redicrected afterwards.
This functionality seems to be missing from the default login.html/login.js causing the user to be redirected to his home page after login, rather then to the deeplink that he opened. While i could hack this into the login.js to function as the previous deeplink modules i believe that this is something that should work out of the box, as now deeplinks seem to fail for users that are not logged in yet and are required to login to use a given deeplink. I believe that Mendix should fix this but what is your take on it?