Ok I think I can explain that. These checkboxes are controlled by the UI. For instance once you use the create directory account it gets unchecked and greyed out. The reason is you really could not create another account in the directory with the same name. The other two get unchecked because you don't necessarily want to do these again next time the account gets saved. So in effect they are "one shot" selections or really just actions. They can be used again but they would need to be manually activated. All these "rules" / UI behavior are not duplicated in imports.
Regards,
Gary