All the maps that i played with so far with FTE, the lava was ok, but I don't know why some of the DM4JAM maps overwrites the water/lava/teleport values.
My solution: check if r_wateralpha is set to 1 AFTER you load the map.
When i was playing "The Dirge of Despair" (dm4jam_bloodshot.bsp) i had to bind a key (right-mouse-button) to "r_wateralpha 1" because everytime i died and quickloaded the map, the lava was invisible again, so i just press the right-mouse-button to bring the lava back.
"Absolutego" (dm4jam_skacky.bsp) also has problem with the water texture in FTE. r_wateralpha is automatically sets to zero when you enter the map, since the map has water all over the place, i choose to play it with quakespasm.
The start map has a problem too. The lava is ok, but the teleport texture is invisible. You can solve this with r_telealpha 1 or 0.5 or something like that (i only discover this solution in my last video) you can see here that the teleport textures are ok with this command
https://www.youtube.com/watch?v=OUb6mLtkE7k
The other maps are ok, i think...