Taxonomic: I'm having the same exact problem. I thought it was due to the CO8 mod (I haven't played the game in a year) and deleted the entire folder and installed vanilla TOEE in a clean directory but I'm still getting the flickering.
To make matters worse, whenever I attempt to change any graphics settings, the game crashes to desktop.
I've found that if you use unsupported resolutions by modifying the game's configuration file, it will crash to desktop. CO8 supports the newer resolutions without crashing, however. I currently run it in 1920 x 1080 with no CTDs.
Even with CO8, the video flashes, so I just quickly press "Esc" to skip past it.