If I leave my load order unchanged and I switch to Doom2.wad the chaingunners appear normal. Only Doom_Complete gives me invisible chaingunners.
I did a little bit of digging since i posted and It seems to be some sort of issue when running Wadsmoosh 1.3 with the NeuralUpscale2x_v1.0 mod. If i disable the Neural upscale everything works as it should. Best i can tell only the Chaingunner has issues, but all looks normal to me when I start digging around in the actual sprite folder. Maybe something to do with the Filter naming?