I would like for them to not just spawn jungles and I tried removing the biomes in the list in the config file, but that doesn't appear to be working and they are still all jungle when I make a new world. I've also tried changing the player spawn biome to another like forest but it still spawns me in a jungle.

If you wanted to spawn in different biome you should change the line:

    # When this is set the player will always spawn in the given biome [default: jungle]
    S:spawnBiome=jungle

change to biome you want or leave it empty so you will spawn randomly

but if you wanted to remove biomes:

lostcity_biosphere {
    # List of biomes that are allowed in the world. Empty list is default all biomes. The factor controls how much that biome is favored over the others (higher means less favored!) [default: [jungle=1], [jungle_hills=1], [jungle_edge=2]]
    S:allowedBiomeFactors <
        jungle=1
        jungle_hills=1
        jungle_edge=2
        taiga=1
	mesa=3
     >

I did a test on lostcities-1.12-2.0.22 and it just worked fine...

Nice thanks