diff --git a/EmoTracker.Data/ApplicationSettings.cs b/EmoTracker.Data/ApplicationSettings.cs
index c3bf92f..1f71dd8 100644
--- a/EmoTracker.Data/ApplicationSettings.cs
+++ b/EmoTracker.Data/ApplicationSettings.cs
@@ -86,6 +86,10 @@ Sessions.SessionSettings ActiveSessionSettings
         /// Called from <see cref="Sessions.TrackerState"/>'s adoption ctor
         /// so a primary state inherits the user's pre-existing preferences
         /// loaded from <c>ApplicationSettings.json</c>.
+        /// Also called from <see cref="Sessions.TrackerState.ActivatePackage"/>
+        /// to reset settings to the saved defaults before init.lua runs,
+        /// ensuring pack scripts start from the user's preferences and may
+        /// optionally override them.
         /// </summary>
         internal void SeedIntoSession(Sessions.SessionSettings target)
         {
@@ -97,6 +101,54 @@ internal void SeedIntoSession(Sessions.SessionSettings target)
             target.PinLocationsOnItemCapture = mbSeedPinLocationsOnItemCapture;
         }
 
+        /// <summary>
+        /// Called by <see cref="Sessions.SessionSettings"/> when a tracked
+        /// property changes, so UI-driven setting changes are persisted to
+        /// <c>ApplicationSettings.json</c> as the new defaults for future
+        /// sessions / pack loads.
+        ///
+        /// <para>
+        /// No-ops when called while a pack is loading (i.e.
+        /// <see cref="Sessions.PackageLoader.IsLoading"/> is true) to avoid
+        /// init.lua-driven changes overwriting the user's saved preferences.
+        /// </para>
+        /// </summary>
+        internal void SyncSeedsFromSession(Sessions.SessionSettings source)
+        {
+            if (source == null) return;
+            if (Sessions.PackageLoader.IsLoading) return;
+
+            bool changed = false;
+            if (mbSeedIgnoreAllLogic != source.IgnoreAllLogic)
+            {
+                mbSeedIgnoreAllLogic = source.IgnoreAllLogic;
+                changed = true;
+            }
+            if (mbSeedDisplayAllLocations != source.DisplayAllLocations)
+            {
+                mbSeedDisplayAllLocations = source.DisplayAllLocations;
+                changed = true;
+            }
+            if (mbSeedAlwaysAllowClearing != source.AlwaysAllowClearing)
+            {
+                mbSeedAlwaysAllowClearing = source.AlwaysAllowClearing;
+                changed = true;
+            }
+            if (mbSeedAutoUnpinLocationsOnClear != source.AutoUnpinLocationsOnClear)
+            {
+                mbSeedAutoUnpinLocationsOnClear = source.AutoUnpinLocationsOnClear;
+                changed = true;
+            }
+            if (mbSeedPinLocationsOnItemCapture != source.PinLocationsOnItemCapture)
+            {
+                mbSeedPinLocationsOnItemCapture = source.PinLocationsOnItemCapture;
+                changed = true;
+            }
+
+            if (changed)
+                WriteSettings();
+        }
+
         public bool IgnoreAllLogic
         {
             get
diff --git a/EmoTracker.Data/Sessions/PackageLoader.cs b/EmoTracker.Data/Sessions/PackageLoader.cs
index a633562..e5379e2 100644
--- a/EmoTracker.Data/Sessions/PackageLoader.cs
+++ b/EmoTracker.Data/Sessions/PackageLoader.cs
@@ -75,6 +75,14 @@ public PackageLoadEventArgs(TrackerState target, IGamePackage package, IGamePack
         [ThreadStatic]
         static bool mInProgress;
 
+        /// <summary>
+        /// True while <see cref="LoadInto"/> is executing on this thread.
+        /// Used by <see cref="ApplicationSettings.SyncSeedsFromSession"/> to
+        /// suppress seed-writes driven by pack-script (init.lua) changes,
+        /// so only explicit user UI changes update the saved defaults.
+        /// </summary>
+        internal static bool IsLoading => mInProgress;
+
         /// <summary>
         /// Loads <paramref name="package"/> (with optional <paramref name="variant"/>)
         /// into <paramref name="target"/>'s catalogs. Caller is responsible for
diff --git a/EmoTracker.Data/Sessions/SessionSettings.cs b/EmoTracker.Data/Sessions/SessionSettings.cs
index 72b648e..089f1fa 100644
--- a/EmoTracker.Data/Sessions/SessionSettings.cs
+++ b/EmoTracker.Data/Sessions/SessionSettings.cs
@@ -54,15 +54,19 @@ public partial class SessionSettings : TransactableModelTypeBase
         public partial bool IgnoreAllLogic { get; set; }
 
         [KVMutable]
+        [OnChanged(nameof(SyncSeedsToApplicationSettings))]
         public partial bool DisplayAllLocations { get; set; }
 
         [KVMutable]
+        [OnChanged(nameof(SyncSeedsToApplicationSettings))]
         public partial bool AlwaysAllowClearing { get; set; }
 
         [KVMutable]
+        [OnChanged(nameof(SyncSeedsToApplicationSettings))]
         public partial bool AutoUnpinLocationsOnClear { get; set; }
 
         [KVMutable]
+        [OnChanged(nameof(SyncSeedsToApplicationSettings))]
         public partial bool PinLocationsOnItemCapture { get; set; }
 
         [KVMutable]
@@ -111,6 +115,12 @@ protected void OnIgnoreAllLogicChanged()
             // ApplicationSettings.IgnoreAllLogic's setter.
             var state = OwnerState as TrackerState;
             state?.Locations.RefreshAccessibility();
+            SyncSeedsToApplicationSettings();
+        }
+
+        protected void SyncSeedsToApplicationSettings()
+        {
+            ApplicationSettings.Instance?.SyncSeedsFromSession(this);
         }
 
         // ----------- Fork support ---------------------------------------------
diff --git a/EmoTracker.Data/Sessions/TrackerState.PackageOps.cs b/EmoTracker.Data/Sessions/TrackerState.PackageOps.cs
index 58615af..9c94ae1 100644
--- a/EmoTracker.Data/Sessions/TrackerState.PackageOps.cs
+++ b/EmoTracker.Data/Sessions/TrackerState.PackageOps.cs
@@ -134,6 +134,11 @@ public void ActivatePackage(IGamePackage package, IGamePackageVariant variant)
                 PackageManager.Instance.RefreshActiveState();
                 NotifyPropertyChanged(nameof(ActiveVariantUID));
 
+                // Reset tracking settings to the user's saved defaults before
+                // running init.lua, so pack scripts start from the user's
+                // preferences and may optionally override them (issue #83).
+                ApplicationSettings.Instance.SeedIntoSession(Settings);
+
                 PackageLoader.LoadInto(this, package, variant);
             }
             finally