Poor frame syncronisation causes screen flickering

[TakuikaNinja]

You are probably very aware of the screen flicker issue.
I had a look at this in Mesen2's event viewer and I can see why it has this problem. Your screen updates are frequently occurring outside of vertical blank. The PPU's VRAM can only be written to safely during blanking (vertical blank at the start of NMI, or forced blanking). During rendering, PPU accesses behave in an unpredictable manner as it is doing its own fetches to draw the screen.

Unfortunately, this seems to be a symptom of much bigger problem - Your program logic does not appear to be synchronised with PPU frames in any way. A more sensible approach on this system would be to implement a Main & NMI handler thread, as recommended by NESdev Wiki:

• https://www.nesdev.org/wiki/The_frame_and_NMIs
• https://www.nesdev.org/wiki/NMI_thread