Are you talking an NG+ run or are you talking a second character? Only one save per playthrough should be able to be imported to ME2, and that is the one that used to trigger when you were entering the hatch at the end of the tram scene, just before facing Saren. I don't know if they altered this to allow the Counselor pick to be saved too, but that is where it used to trigger. If you are showing more than one save allowed to be imported into ME2 for a character, then one is original play and the other is NG+ run. If you are talking separate characters, then it should list them separately. IF you haven't already done a repair on your install, I would do so, and then maybe try another run on the ending to see if it triggers.
You can have more than one to choose from if you load a save from before the final confrontation and then finish it again. No need for NG+. I have 3 saves to choose from (1 Udina and 2 Anderson)..
