TL;DR: Don't use WildNature with Waystones. I took a guess that WildNature was the problem.. I think their biome generation (of most of their custom biomes, not all) wipes out whatever would be there and constructs theirs in its place, resulting in the loss of the Waystones.

Hey hey. First off, loving the concept so far, it's pretty much exactly what I was looking for (landmarks that you can teleport from one to another, to add some restriction and balance to teleporting)

I'm playing on 1.14.4, and I'm wondering if the waypoints are supposed to be spawning randomly around the world (I've set the chunk distance between them to 20, 5 and 1 to test).. so far, I've only gotten them to spawn in villages with the other config option (although it has spawned three in a single village..)

I haven't done any major testing to see if there's a mod conflict, I'm wondering if this is something you already know about and might be already working on. Happy to test things out more if necessary. Current list of mods is below. Cheers!

Ageing-Mobs-1.14-1.0.1.jar
AmbientSounds_v3.0.14_mc1.14.4.jar
anviltweaks-1.4b.jar
Aquaculture-1.14.4-2.0.7.jar
AttributeFix-1.14.4-3.0.2.jar
AutoRegLib-1.4-35.jar
backpacked-1.4.0-1.14.4.jar
Berry-Good-1.14.4-v1.0.3.jar
betteranimals-1.14.4-5.2.1.jar
betteranimalsplus-1.14.4-8.2.1.jar
BetterCaves-1.14.4-1.1.1.jar
BetterShieldsMC1.14.4-1.1.jar
BetterSprinting-1.14.4-v3.0.1a.jar
bettertridentreturn-1.14.4-1.0.0.jar
BonsaiTrees-2.0.2.35.jar
CarryOn-v1.12.4.jar
ChickenDropFeathers-2.0.jar
chunkloader-1.14.4-1.0.0.jar
classicbar-2.0.0a.jar
cofh_core-1.14.4-0.2.0b.jar
copypaste-1.4.jar
cosmeticbeds-FORGE-1.14.4-2.0.0.1.jar
CraftingCraft_1.14.4-7.1.7.jar
Craft_and_Hunt_V0.9.3_MC_1.14.4.jar
create-mc1.14.4_v0.1.1a.jar
Cucumber-1.14.4-2.0.6.jar
cursedearth-1.4a.jar
CyclopsCore-1.14.4-1.6.1.jar
Disenchanting_(forge)_1.14.4-1.2.0.jar
dispensebreaker-1.14.4-1.0.jar
DoubleSlabs-1.14-1.0.0.jar
Durability101-1.14-0.0.3.jar
Dynamic_Surroundings-MobEffects-0.0.4.0.jar
Dynamic_Surroundings-SoundControl-0.0.4.0.jar
Easy+Commands.jar
ensorcellation-1.14.4-0.2.0b.jar
EverlastingAbilities-1.14.4-1.6.0.jar
extlights-1.8.jar
extraboats-1.2.3-1.14.4.jar
fishtraps-0.0.4.jar
globalxp-1.14.4-v1.4.10.jar
Grass_Seeds-1.1.jar
grindst_1.14-1.2.jar
healingcf_1.14-1.7.jar
horsestats-1.14.4-1.0.1.jar
Hwyla-forge-1.10.6-B67_1.14.4.jar
inftrading_1.14-1.0.jar
invtotem_1.14-1.0.jar
invtweaks-1.14.4-0.6.1.jar
ironchest-1.14.4-9.1.5.jar
ironfurnaces-1.14.4-1.7.0.jar
jei-1.14.4-6.0.0.27.jar
JustEnoughResources-1.14.4-0.10.0.70.jar
LargeFluidTank-14.9.4.jar
libnonymous-1.14.4-1.0.4.25.jar
LootingModMC1.14.4-1.0.2.jar
mining-helmet-1.14.4-1.0.4.jar
MixinBootstrap-1.0.1.jar
Mooshroom_Tweaks-1.0.jar
Neat+1.5-19.jar
nhacampfire_1.14-1.5.jar
nifty-1.14.4-2.8.jar
Nutritious_Milk-1.0.jar
OptiFine_1.14.4_HD_U_F5.jar
OreExcavation-1.6.147.jar
Pet_Names-1.0.jar
PickleTweaks-1.14.4-3.0.7.jar
Quark-r2.0-209.jar
quartz-chests-1.0.0.3.jar
QuickLeafDecay-MC1.14.4-1.2.5.jar
RefinedRelocation_1.14.4-6.2.6.jar
ruins-1.14.4.6.jar
run.bat
SaveMyStronghold-1.14.4-1.0.0.jar
SBM-WoodenShears-1.14.4-1.0.0.jar
ScalableCatsForce-2.13.1-build-6-with-library.jar
simpleores-1.14.4-2.0.6.0.jar
simplylight-0.9.0.jar
Snowballs_Freeze_Mobs-1.0.jar
Softer_Hay_Bales-1.0.jar
Spice_of_Life-Carrot_Edition-1.9.3.jar
Spiders_Produce_Webs-1.0.jar
swingthroughgrass-1.14.4-1.3.2.jar
The-Endergetic-Expansion-1.14.4-v1.1.1.jar
ToolBelt-1.14.4-1.12.5.jar
torchslabmod-1.14.4_v1.4.jar
Trapcraft-1.14.4-2.6.1-universal.jar
TrashSlot_1.14.4-10.4.8.jar
unclegglass-2.0.0-1.14.4.jar
upsizer-mc1.14.4-5.0b4.jar
valhelsia_structures-1.14.4-0.0.2a.jar
VanillaTweaks-1.14.4.1.5.12.jar
VillagerNames-1.4.jar
VillageSpawnPoint-1.0.jar
walljump-1.14.4-1.3.1.jar
Waystones_1.14.4-5.1.0.jar
Weaker_Spiderwebs-1.2.jar
WesserboysOverlays-1.0.0.1-1.14.4.jar
WildNature-2.1.3.jar
XaerosWorldMap_1.5.4.jar
Xaeros_Minimap_20.1.0.jar
Zombie_Villagers_From_Spawner-1.0.jar