Certain missions in the original Syndicate appear with a green tileset, as well as green skin for the NPCs that have skin visible. The most recent example is Brazil - No matter what I set the output to in the conf file (overlay, ddraw, opengl), the green is there.

I checked a longplay video on Youtube for this same mission, and the green is present in that video too: https://youtu.be/ACVZ5b8wW14?t=19422 (look at the skin of the NPCs in the top-right corner and bottom of the screen). I assume this player is using the GOG build also, since the video was uploaded just last year.

Does anyone know if this was intentional on the developer's part, or could it be a bug with this build of the game? If intentional it seems like an odd decision to me, since it makes the NPCs in these missions look like zombies.

I don't know the reason but also the orignal game back in '93 had "green levels". I guess was an "artistic" choice.

Syndicate for the PC only uses a 16 color screenmode (I think VGA 640x400 or 640x480) and not a similar SVGA-mode with 8 Bit colordepth. There are not many games with highres-VGA, I only remember one more game, Battle Bugs by Sierra (1994?).

I think they changed the color palette in some missions to give them an unique look. If you use the same palette in every mission they all look the same and might geht boring after a while.

The Amiga version is more colorful and uses 32 colors, but only in 320x256.