ZDoom

This happens in the palette versions of both the Carmack and Softpoly renderers. Curiously, this only happens when models are turned on- when models are off the voxel models have correct colors even in these renderers.

Models on:


Models off:


Test wad used:
http://teamhellspawn.com/zdoom_vox.zip

If you look at the Chaingun, you can notice they seem to be drawn differently - the one with models enabled is more... Cube-ey.
Which leads to the conclusion that what's happening here is that it's trying to render the OpenGL renderer's mesh conversions instead of using the normal voxel rendering code.
Unfortunately, the renderers are not my area of expertise, so I can't tell you why it's doing that, nor can I fix it.