Basically, all font colors seem to look different depending on the IWAD being played. This image shows Doom, Heretic and Hexen side by side. The colors used to be equal before, in 4.6.1.
The mod to test this display is here.
Fixed. There was a slight deviation in the luminosity calculation because this did not treat color index 0 of the palette properly.
This now completely skips the palette to avoid the problems.