Could you try clearing your cache manually by disabling the option and restarting the game, then re-enabling the option and seeing if the issue persists?
Because this is all that I have in my log file that isn't mipmapped properly when I load the full suite of mods I reskin:
37.395 Parallel Sprite Loader initialized (threads: 23)
37.513 Warning! Sprite at {0,0; 128x128} from __Dectorio__/graphics/technology/basic-wall.png is defined with 4 mipmap levels, but level 1 is expected to be at {128,0; 64x64} which is out of bounds of the source image.
43.437 Warning! Sprite at {0,0; 128x128} from __bobelectronics__/graphics/icons/technology/advanced-electronics-2.png is defined with 4 mipmap levels, but level 1 is expected to be at {128,0; 64x64} which is out of bounds of the source image.
43.437 Warning! Sprite at {0,0; 128x128} from __bobelectronics__/graphics/icons/technology/advanced-electronics.png is defined with 4 mipmap levels, but level 1 is expected to be at {128,0; 64x64} which is out of bounds of the source image.
43.437 Warning! Sprite at {0,0; 128x128} from __bobelectronics__/graphics/icons/technology/electronics.png is defined with 4 mipmap levels, but level 1 is expected to be at {128,0; 64x64} which is out of bounds of the source image.
43.549 Warning! Sprite at {0,0; 128x128} from __mini-machines__/graphics/technology/mini-beacon.png is defined with 4 mipmap levels, but level 1 is expected to be at {128,0; 64x64} which is out of bounds of the source image.
44.561 Sprites loaded