After some more experimenting, I noticed that after a clean install it would work the first time, but never again. Also, I noticed that if I set the refresh rate in the basiliskii.cfg file to dynamic (frameskip 0) and constantly moved my mouse it wouldn't give me the error. What would happen is the screen would turn completely white and then as I moved the mouse it would replace horizontal chunks with the emulator screen. I could do this until all of the screen was visible, but when I tried to shut down, the screen would go black, the mouse would invert color and I could not close the emulator or reboot.
Please do not post a support request without first reading and following the advice in https://retropie.org.uk/forum/topic/3/read-this-first