Hey guys, I know this is old but I wanted to respond since I had the same issue. I had the hd movies (640 x 480 @59) from emumovies and they would lag after a few seconds, but only certain games. I found the solution by reformatting them from 59 frames per second to 30 fps. I used a free program called winx video converter. It was fast to convert and now all of the videos play great.
Guess the software renderer can't keep up. The hd AM intro vid dies on the pi 3 so this all makes sense. I'll just convert everything to 30 fps which is almost indistinguishable from 59 because most old games ran at a locked 30 anyways. File size is 1/3 as well.