Well, I tested the game without AM and their free will returned to normal. I'm thinking it's conflicting with one of my mods (I have like 20 mods installed). When I have time, I'm going to run the game with only AM and twallan's Master Controller (because it's confirmed that they don't conflict) and see what happens.

My hypothesis is that it might be conflicting with twallan's Story Progression because I noticed that inactive sims' free will has also been affected. Even though I didn't turn on AM's story progression, it might still be a problem.

When I installed this mod into my game, I noticed that my sims' free will has been modified. It seems like they stand idly more often, waiting for me to tell them what to do. On seldom occasions, they would act on their own. I made one of my sims visit another family's house to observe their behavior. I observed the nonactive family and they just stood around the living room, complaining that they need to go to sleep. Then, they would fall on the floor because of their lack of energy.
The only features that I have enabled for this mod are:
NoKillWantsOnUnselect
NoRouteFail
NoAdultMoveRequirement
ShowNumericalValues
UseHigherPrecisionTime
TrackAllMovingCars
UnifiedBilling
NoInventoryDestruction
LawOfConservationOfMass
NoPsychicCurfewPolice
AllowNPCAspirationGain
FulfillWantsWithoutLocking
NonActiveTraitLearnings
NoAutomaticSchool
AllowInactivePerfGain
BetterVehicleDisembark
AllIngredientsEdible
NoAdultCASRequirement
BetterBBObjectInfo

Do I need to turn anything on (or off) for my sims' free will to return back to normal?