I do not know what this sentence: "Same clip imports completely into After Effects." means, but as for the first part, I've encountered the same problem myself.  Play the clip and pay attention to the speed.  I'm betting the video plays approximately twice as fast as it should, and the audio goes on until the end.  If that describes your problem, here is what I do in this case, first, in the timeline mode, left click the video so it's selected (red) then click "ungroup" (the broken chain icon).  Cut off & delete the second half of the video that is just that one lingering frame.   Then right click the video portion and select "video effects".  From there you can slow the speed of the video down until it ends at the same place as the audio.  You might not get it to line up perfectly, but you should be able to get close enough.