If an item has the +FLOORCLIP flag and it is sitting on a 3D floor with a non-floorclipping texture on it, but the 3D floor is above a texture that has a floorclipping terrain, the item will ink into the bridge.

As you can see from that image, the serpent torches (modified DECORATE to have +FLOORCLIP - they don't have it by default) that are sitting on the wooden pedestals are fully visible. The one sitting in the water floor-clips as expected, but the one on the bridge also floorclips.
I tried placing some Clinks/Sabreclaws on there and they didn't seem to show the issue (and they do floorclip by default).

So I thought that it might be something to do with me having smart sprite clipping on. On messing with the settings, the only one that made a difference at all was when I set it to "smarter" the central torch rose up a little, but it still wasn't sitting on top of the bridge properly.
I first noticed this in an actual map where there was a 3D bridge something like a massive 3000 units above a floor-clipping liquid and all the pickups and decorations on the bridge were sinking into it.
Example file attached - the one from the screenshot with the modified serpent torches.