For some reason lightroom keeps forgetting the settings on the import dialog boxes. I set the options I want, but they are forgotten when I go back and do another Import (sort order and organize into one folder are always unselected). In order to fix this create a new preset with the sort order and organizing to one folder selected and save the preset.
The next time you use the import dialogue the import settings on the screen will default to none however the sort order and the organize into one folder is retained from one session to the next.