diff --git a/MobiFlight/Controllers/ControllerBindingService.cs b/MobiFlight/Controllers/ControllerBindingService.cs
index ecfd35fe4..c92ddd289 100644
--- a/MobiFlight/Controllers/ControllerBindingService.cs
+++ b/MobiFlight/Controllers/ControllerBindingService.cs
@@ -34,7 +34,7 @@ public List<ControllerBinding> AnalyzeProjectBindings(Project project)
                 results.ForEach(b =>
                 {
                     // Only add if not already present (first occurrence wins)
-                    if (!allResults.Any(existing => existing.OriginalController == b.OriginalController))
+                    if (!allResults.Any(existing => existing.OriginalController.AreEqual(b.OriginalController)))
                     {
                         allResults.Add(b);
                     }
@@ -66,7 +66,7 @@ public virtual List<ControllerBinding> PerformAutoBinding(Project project)
 
                 foreach (var binding in results)
                 {
-                    var bindingExists = allResults.FirstOrDefault(b => b.OriginalController == binding.OriginalController);
+                    var bindingExists = allResults.FirstOrDefault(b => b.OriginalController.AreEqual(binding.OriginalController));
                     // Only add if not already present (first occurrence wins)
                     if (bindingExists != null) continue;
 
@@ -76,7 +76,7 @@ public virtual List<ControllerBinding> PerformAutoBinding(Project project)
                 // Update binding mappings for next config file
                 foreach (var mapping in serialMappings)
                 {
-                    if (appliedBindingMappings.FirstOrDefault(b => b.BoundController == mapping.BoundController) != null) continue;
+                    if (appliedBindingMappings.FirstOrDefault(b => b.BoundController.AreEqual(mapping.BoundController)) != null) continue;
 
                     appliedBindingMappings.Add(mapping);
                 }
diff --git a/MobiFlightUnitTests/MobiFlight/Controllers/ControllerBindingServiceTests.cs b/MobiFlightUnitTests/MobiFlight/Controllers/ControllerBindingServiceTests.cs
index 889104818..6d1718764 100644
--- a/MobiFlightUnitTests/MobiFlight/Controllers/ControllerBindingServiceTests.cs
+++ b/MobiFlightUnitTests/MobiFlight/Controllers/ControllerBindingServiceTests.cs
@@ -468,6 +468,29 @@ public void AnalyzeProjectBindings_MultipleConfigFiles_AnalyzesAll()
             Assert.AreEqual(ControllerBindingStatus.AutoBind, binding2.Status);
         }
 
+        [TestMethod]
+        public void AnalyzeProjectBindings_MultipleConfigFiles_WithSameController_AnalyzesAll()
+        {
+            // Arrange
+            var project = new Project();
+            project.ConfigFiles.Add(CreateConfigFileWithController("Board1/ SN-111"));
+            project.ConfigFiles.Add(CreateConfigFileWithController("Board1/ SN-111"));
+
+            SetupConnectedControllers(new[]
+            {
+                ("Board1", "SN-111"),
+                ("Board2", "SN-333")
+            });
+
+            // Act
+            var result = service.AnalyzeProjectBindings(project);
+
+            // Assert
+            Assert.HasCount(1, result);
+            var binding1 = result.Find(b => b.OriginalController.Equals(SerialNumber.CreateController("Board1/ SN-111")));
+            Assert.AreEqual(ControllerBindingStatus.Match, binding1.Status);
+        }
+
         [TestMethod]
         public void PerformAutoBinding_MultipleConfigFiles_UpdatesAll()
         {
@@ -597,6 +620,48 @@ public void AnalyzeProjectBindings_MixedControllerTypes_AnalyzesAll()
 
         #endregion
 
+        #region Test with multiple configFiles in project
+        [TestMethod]
+        public void AnalyzeProjectBindings_MultipleConfigFiles_SameController_AutoBind()
+        {
+            // Arrange
+            var project = CreateProjectWithControllersAndMultipleConfigFiles(new[]
+            {
+                "X1-Pro/ SN-1111111111"
+            });
+            
+            SetupConnectedController("X1-Pro", "SN-9876543210");
+            
+            // Act
+            var result = service.AnalyzeProjectBindings(project);
+            
+            // Assert
+            Assert.HasCount(1, result, "There should only be one controller binding");
+            var binding1 = result.Find(b => b.OriginalController.Equals(SerialNumber.CreateController("X1-Pro/ SN-1111111111")));
+            Assert.AreEqual(ControllerBindingStatus.AutoBind, binding1.Status);
+        }
+
+        [TestMethod]
+        public void AnalyzeProjectBindings_MultipleConfigFiles_SameController_Missing()
+        {
+            // Arrange
+            var project = CreateProjectWithControllersAndMultipleConfigFiles(new[]
+            {
+                "X1-Pro/ SN-1111111111"
+            });
+
+            SetupConnectedController("Other Controller", "JS-9876543210");
+
+            // Act
+            var result = service.AnalyzeProjectBindings(project);
+
+            // Assert
+            Assert.HasCount(1, result, "There should only be one controller binding");
+            var binding1 = result.Find(b => b.OriginalController.Equals(SerialNumber.CreateController("X1-Pro/ SN-1111111111")));
+            Assert.AreEqual(ControllerBindingStatus.Missing, binding1.Status);
+        }
+        #endregion
+
         #region Helper Methods
 
         private Project CreateProjectWithController(string moduleSerial)
@@ -613,6 +678,19 @@ private Project CreateProjectWithControllers(string[] moduleSerials)
             return project;
         }
 
+        private Project CreateProjectWithControllersAndMultipleConfigFiles(string[] moduleSerials)
+        {
+            var project = new Project();
+            var configFile = CreateConfigFileWithControllers(moduleSerials);
+            project.ConfigFiles.Add(configFile);
+
+            configFile = CreateConfigFileWithControllers(moduleSerials);
+            project.ConfigFiles.Add(configFile);
+
+            project.Sim = "msfs";
+            return project;
+        }
+
         private ConfigFile CreateConfigFileWithController(string moduleSerial)
         {
             return CreateConfigFileWithControllers(new[] { moduleSerial });