There is no fix because I cannot reproduce that problem, it affects only used which use either Network Extensions 2 or Metro Overhaul Mod or both, but flickering occurs also without FPS Booster which seem to work as a trigger for the issue and the root cause is in one of mentioned mods.

I noticed it wasnt because of your mod. it was because of patch loader mod, but the other mods you mentioned could be part of the problem as well.

Sorry, but It's impossible. Patch Loader doesn't do anything other than patching the game with the patch files the FPS Booster has. Without Patch Loader mod, FPS Booster won't do anything alone because the core thing of the mod is to patch the game and only Patch Loader mod can process those patches.

Do you have Metro Overhaul or Network Extension 2? Maybe it's worth trying to run in ghost mode (enable in MOM settings, before loading savegame, it will temporarily disable the mod)

Yes I have both of these mods. I can ditch the metro overhaul mod but i dont think i'm willing to disable network extension 2

I'd test one run with MOM disabled (ghost mode) to see if changed anything or not

This is one year later, but I've confirmed that the flickering happens when Metro Overhaul is active.