Are they fixed in the 2d view or move in relation to it? Does it move or exist in the 3d world? Did SH3 work correctly before? Are these artifacts appearing sudden, or at some point into the game? A bit more description on how they occur would help perhaps.
Did you recently change or update graphics drivers?
If not related to the the last option, if you have no other mods applied anymore or atleast as far as you can remember after undoing mods. Then I'd regard this as a corrupted installation and try to re-install.
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