The title is pretty self-explanatory. It doesn't happen with all mods though.
We own a 1.7.10 forge server. Thaumcraft 4 works fine, investigations are saved when leaving the server, but Galacticraft (v 3.0.12.504) and AdvancedLightsabers (v 1.2.2) progress is deleted every time the server is turned off, Galacticraft team flags disappear and players lose all abilities gained from AdvancedLightsabers' holocrons.
Regular Minecraft archievements also reset from time to time, but we haven't looked into that because it doesn't really affect gameplay. We all own premium Minecraft accounts.
Software:
1.7.10-Forge10.13.4.1614-1.7.10
Server Mods:
files/mods/
AdvancedLightsabers-1.7.10-1.2.2.jar
ArchimedesShips-1.7.1.jar
backpack-2.0.1-1.7.x.jar
BiblioCraft[v1.11.7][MC1.7.10].jar
chocolateQuest-1.7.10-1.0.jar
CodeChickenCore-1.7.10-1.0.7.47-universal.jar
CustomMobSpawner 3.3.0.zip
download (I don't know where this file came from or what it does, it's not in my personal mods folder)
DrZharks MoCreatures Mod v6.3.1.zip
fossilsarcheology-7.3.2.jar
GalacticraftCore-1.7-3.0.12.504.jar
Galacticraft-Planets-1.7-3.0.12.504.jar
HardcoreEnderExpansion MC-1.7.10 v1.8.6.jar
llibrary-1.5.1-1.7.10.jar
Mantle-1.7.10-0.3.2b.jar
MCA-1.7.10-5.2.2-universal.jar
MicdoodleCore-1.7-3.0.12.504.jar
RadixCore-1.7.10-2.1.3-universal.jar
Thaumcraft-1.7.10-4.2.3.5.jar
twilightforest-1.7.10-2.3.7.jar
files/mods/1.7.10/ (this directory is created automatically, both in the server files and in our mods folders)
Baubles-1.7.10-1.0.1.10.jar
CodeChickenLib-1.7.10-1.1.3.138-universal.jar
Any ideas on what may be causing this problem?
Edit: forgot to add that Rei's minimap waypoints also reset (the mod doesn't appear on the list because it's client-side). Galacticraft and AdvancedLightsabers were recenly added to the server but I've been using Rei's minimap since the beginning and waypoints aren't saved when the server is closed. Other features from the mods that were added after creating the world work just fine.