The only mod I'm aware of that causes this is Enhanced Gameplay (EGP), though I'm sure there are others.
Can you test loading with just Sim Settlements to see if they go back to your town? If they do, you just need to start testing without mods to find the culprit.
The only other settler mod is "better settlers" my ammo doesn't have weight but I think that's due to the difficulty setting and with over 177 mods installed right now I might break my game by trying that. I do seem them at their stations every once in a while, but there is never a time in the day where I see all shops manned, farms being tended to and guards at their post. I have all auto assign options turned on ect. Here is my load order for reference just in case you see a red flag that might be causing this.
Fallout4.esm=1
DLCRobot.esm=1
DLCworkshop01.esm=1
DLCCoast.esm=1
DLCworkshop02.esm=1
DLCworkshop03.esm=1
DLCNukaWorld.esm=1
Unofficial Fallout 4 Patch.esp=1
ArmorKeywords.esm=1
SettlementKeywords.esm=1
Homemaker.esm=1
SpringCleaning.esm=1
HUDFramework.esm=1
TrueStormsFO4.esm=1
SimSettlements.esm=1
Faster Terminal Displays (20x).esp=1
QuickTrade.esp=1
LongerPowerLines3x.esp=1
dD-Realistic Ragdoll Force.esp=1
KSHairdos.esp=1
AzarPonytailHairstyles.esp=1
ImmersiveVendors.esp=1
Publick Occurrences Expanded.esp=1
PD_VisualReload.esp=1
BetterSettlers.esp=1
BetterSettlersCleanFacePack.esp=1
BetterSettlersMortalPack.esp=1
BetterSettlersNoLollygagging.esp=1
Insignificant Object Remover.esp=1
SimSettlements_VIS.esp=1
SC_ExpandedScrapList.esp=1
TimerPowerSwitch.esp=1
WVSimSAddon.esp=1
OWR_CraftableDecor.esp=1
OWR_CraftableDecor_CW.esp=1
OWR_CraftableDecor_SKPatch.esp=1
BetterModDescriptions.esp=1
BetterModDescriptions223P.esp=0
ARWCSM - 2 - Full - Vanilla Weights.esp=1
No more monochrome - Color setting for the Pipboy!.esp=1
LooksMenu.esp=1
CROSS_GoreCrits.esp=1
CROSS_GoreCrits_FarHarborPatch.esp=1
BetterNightVision.esp=1
DarkerNightsDetection.esp=1
BossChestsHaveLegendaries.esp=1
AA Better Companions - No Conflicts.esp=1
EveryonesBestFriend.esp=1
VisibleCompanionAffinity.esp=1
BetterGenerators.esp=1
Crafting Workbench.esp=1
FunctionalDisplays-Collectibles.esp=1
FunctionalDisplays.esp=1
FunctionalDisplays-MISC-Vanilla.esp=1
Give Me That Bottle.esp=1
FunctionalDisplays-Patch-DLC-ALL.esp=1
OCDecorator.esp=1
OCDecoratorDLC.esp=1
OCDispenser.esp=1
BetterJunkFences.esp=1
True Legendary Enemies.esp=1
EnhancedLightsandFX.esp=1
MoreUniques.esp=1
Armorsmith Extended.esp=1
funcweddingrings.esp=1
DiamondCitySWAT.esp=1
RaiderOverhaul.esp=1
ImprovedBoS.esp=1
LoreFriendlySurvivalChems.esp=1
BetterModDescriptionsROWIP.esp=1
ShipwreckIsle.esp=1
Grunts.esp=1
BetterModDescriptionsAE.esp=1
Crimsomrider's Tomb Raider Accessories.esp=1
GlovesOfTheCommonwealth.esp=1
dD-Enhanced Blood.esp=1
PowerLinePhysics.esp=1
AnS Wearable Backpacks and Pouches.esp=1
AnS Wearable Backpacks and Pouches - Ballistic Weave.esp=1
AnS Wearable Backpacks and Pouches - Power Armor Carry Capacity.esp=1
Ammo.esp=1
chem redux.esp=1
Swinging Meat Bags.esp=1
TrueStormsFO4-FarHarbor.esp=1
TrueStormsFO4-EarlierSunsets.esp=1
TrueStormsFO4-EarlierSunsetsFH.esp=1
TrueStormsFO4-NukaWorld-FH-Compat.esp=1
DarkerNights.esp=1
TrueReporter.esp=1
Live Action Handy.esp=1
DYNAVISION.esp=1
A Sensible Prydwen Overhaul.esp=1
nvvault1080.esp=1
FortSamson.esp=1
FAR.esp=1
Evan_Modular Kitchen.esp=1
Quieter Settlements - Contraptions.esp=1
Quieter Settlements - Vanilla.esp=1
Quieter Settlements - Wasteland Workshop.esp=1
Piper Natural mom.esp=1
VC_BetterWorkshopLightsComplete.esp=1
VC_BetterWorkshopLightsCW.esp=1
VC_BetterWorkshopLightsVanilla.esp=1
VC_BetterWorkshopLightsWW.esp=1
EasyLockpicking.esp=1
FemsheppingsLightBrawlerOutfits.esp=1
WSB.esp=1
Combat_Helmet_Illumination 1.2.esp=1
Brotherhood of Steel Kit.esp=1
HomePlateConnected.esp=1
Eli_Armour_Compendium.esp=1
My_Minutemen.esp=1
ImmersiveDrumlinDiner.esp=1
SpringCleaningCompatibilityPatch.esp=1
SuperMutantOverhaul.esp=1
PlaneWreck.esp=1
Vivid Waters.esp=1
UniqueUniques.esp=1
Mercenary.esp=1
RRShuttersAndDoors.esp=1
IMG_Castle_Wall_Patches.esp=1
BostonAirport_WorkshopFix.esp=1
DOOMThatGun.esp=1
salvagebeacons.esp=1
OWR.esp=1
NanotechWaterpump_FoodWaterHappy.esp=1
rpampas.esp=1
RobotFactionPaint.esp=1
ProvisionerUniform.esp=1
ProvisionerBackPack.esp=1
You Talk Too Much.esp=1
LooksMenu Customization Compendium.esp=1
wasterArmor.esp=1
M14.esp=1
M14 - AWKCR-Compatibility.esp=1
3dscopes.esp=1
3dscopes-AddToSpawnList.esp=1
3dscopes-framework.esp=1
3dscopes-m14addon.esp=1
3dscopes-FarHarbor.esp=1
3dscopes-NukaWorld.esp=1
Magnolia.esp=1
CBBE.esp=1
BetterSettlersCCAPack2.0.esp=1
Lacy Underwear.esp=1
RRP4APA.esp=1
Expanded Railway Rifle Mods.esp=1
railroad_uniform.esp=1
railroad_uniform_leveledList.esp=1
FlaconOil HD ReTexture_High Quality Pack_Part_1.esp=1
FlaconOil HD ReTexture_High Quality Pack_Part_2.esp=1
PlatinumCurieV2.1.esp=1
FunctionalDisplays-AID-Vanilla.esp=1
MiscHairstyle.esp=1
Ellie remake.esp=1
SimSettlements_XPAC_IndustrialRevolution.esp=1
Minuteman_CB.esp=1
CWSS Redux.esp=1
Settler Sandbox Overhaul.esp=1
Vault-tec brighter lights.esp=1
powerful.50 .esp=1
LongRangeBulletHoles.esp=1
Immersive HUD.esp=1
Wasteland Workshop Streetlights.esp=1
RadUnclechubbyTS.esp=1
RainUncleChubby.esp=1
K9TacticalHarness.esp=1