All textures, model skins etc are in PNG format and so the game palette should not affect them. The area in question is lit using coloured sector lighting and a dynamic light. The mid-texture-like structure is actually a model. When the game is run using any Doom IWAD (doom.wad, doom2.wad, tnt.wad, plutonia.wad), the model is coloured much as I expect it to be. However, in any other game that I have tried, the model looks a little bit off colour.
[spoiler]Doom - looks about right:

Heretic - model looks a bit yellowy

Hexen - much the same

Strife - again, much the same

Harmony

Even Strife with the Doom palette and colormap loaded in a PWAD

And Chex, which surprised me

HacX too

But FreeDoom was OK

So, anyone know why this is? I'm guessing that there is a configuration setting somewhere that handles this situation slightly differently when the game is in Doom mode. I'm just intrigued to find out what it might be.