Not 100% sure how this happens but after some testing here is what I found:
If you are using two mods with their worlds in the root Worlds folder: MyMod/Worlds/MyWorld.et and a scenario that uses that world it can cause servers to not start with this error:
"No game mode present in the world, using fallback logic"

I guess this is cause the layers in the Layer folder get overridden by the mods? Might not be a bug but maybe it could be prevented to save worlds directly in the root Worlds folder with an error message: "Use a sub folder with a unique name". Its also not documented on the wiki to save in a separate folder.

I made a mod to test this (Empty world in root worlds folder with default layer): https://reforger.armaplatform.com/workshop/5DB4F591031D2CEB-DefaultLayerTest
Another mod that has the worlds in the root world folder: https://reforger.armaplatform.com/workshop/5D8753312044580E-ConflictPVERemixedRHS (v0.9.2)
-> "scenarioId": "{98D1DA94DD085045}Missions/ConflictPVERemixedRHS.conf"