I don’t know about you but I had been having an issue where text boxes and the bottom screen wont correctly load, only the text would (Can be seen in this video here: https://www.youtube.com/watch?v=z4ONz9ip6JA&t) as well as that during battles the Top screen would appear on the bottom screen. My fix for this problem is to go to Emulation>Configure>Graphics and turn off Accurate Hardware Shader. Now this will impact performance if you’re on Intergrated Graphics (Like I am) So just turn down the upscalling a bit. With this on I had full speed at 3x Native Graphics now with this off it runs at around 80-100% speed depending on the area.
Although My specs are
System: Lenovo Thinkcentre E73
CPU:Intel Core i3-4150
GPU: Intergrated Graphics ~ Intel HD 4400
Well anyway I hope this solves the problem if you yourself had it.