It doesn’t seem to have anything to do with the source footage or resolution.
I just did a test where I rendered out a 10 frame sequence, just a solid with the number effect labeling the frames 1 thru 10. In quicktime each frame is accounted for. When I bring that rendered quicktime into AE and drop it into a comp, It makes a 10 frame sequence but goes 1,1,2,3,4,5,6,7,8,9. I tried it both at 720 and 1080.