If your record isn't at the end of the play through it wont carry over. You can't be like halfway through a new game plus. It needs to be a completed record. Otherwise if it still doesn't work I guess you're boned.
It kinda is a big deal when one of the reasons to keep your Mass Effect file to transfer Mass Effect 2 was the choices you make would impact stuff in the second one, and even they kinda screwed that up.