Don’t know about the pixel problems, but can help you with the popup window problem about memory, etc.
You need to reboot when you see those windows appear. In fact, if you are dealing in large project with lots of source material, then I suggest rebooting every 3 hours. This is what I am doing with my current project, which is quite long (over 2 hours), and with about 50 hours of source material.
It is better to reboot BEFORE those popup windows occur.