Crisis Core Graphical Glitch Help

[LunaMoo]

You have simulate block transfer effects disabled which is bad, can and will cause glitches, also re-enabling it might not fix what's already glitched until you restart emulation and reload the game from normal in-game save with it active since those effects can be loaded way earlier than when they show.

Second thing, why are you using D3D9? Is that the only backend you can use? If the above wasn't the culprit, this is, since it's the least compatible backend, kept only for performance& compatibility with some old intel graphics that either didn't supported anything else or performed poorly outside of it, on modern and/or dedicated graphics it should be avoided as it's really outdated and some effects are impossible to be emulated correctly using this backend. If you can switch to another one and it doesn't tank your fps, do it, as glitches with forever hunt that backend, otherwise you'll have to accept some problems until you get more modern hardware.

I'd recommend downloading latest version since 1.11.3 is pretty ancient by now. Either last stable 1.12.3 or latest version from buildbot, but I doubt it will help as your problem is probably related to one of the two above.