Thanks to github user @chambm for this amazing patch:

		Universal click-through block for IMGUI windows on PAW / uGUI
		Only works if Harmony is installed
	Added a check to prevent the global.cfg from begin rewritten every time game settings change

Author: linuxgurugamer

Changelog.txt

@@ -1,5 +1,11 @@
 ChangeLog
 
+2.1.20.23 (unreleased)
+	Thanks to github user @chambm for this amazing patch:
+		Universal click-through block for IMGUI windows on PAW / uGUI
+		Only works if Harmony is installed
+	Added a check to prevent the global.cfg from begin rewritten every time game settings change
+
 2.1.20.22
 	Updated version file to use github for version info
 	Copied webpage to README.md

ClickThroughBlocker.version

@@ -10,7 +10,7 @@
     "MAJOR": 2,
     "MINOR": 1,
     "PATCH": 10,
-    "BUILD": 22
+    "BUILD": 23
   },
   "KSP_VERSION_MIN": {
     "MAJOR": 1,

ClickThroughBlocker/AssemblyVersion.cs

@@ -5,6 +5,6 @@
 
  using System.Reflection;
 
- [assembly: AssemblyVersion("2.1.10.21")]
- [assembly: AssemblyFileVersion("2.1.10.21")]
+ [assembly: AssemblyVersion("2.1.10.22")]
+ [assembly: AssemblyFileVersion("2.1.10.22")]
  [assembly: KSPAssembly("ClickThroughBlocker", 2, 1, 0)]

ClickThroughBlocker/OneTimePopup.cs

@@ -147,8 +147,21 @@ static string GlobalDefaultFile
                 return Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location) + "/../Global.cfg";
             }
         }
+
         static internal void SaveGlobalDefault(bool focusFollowsClick, bool universalClickBlocking)
         {
+            if (System.IO.File.Exists(GlobalDefaultFile))
+            {
+                ConfigNode currentNode = ConfigNode.Load(GlobalDefaultFile);
+                bool ffb = false, ucb = false;
+                if (currentNode.TryGetValue("focusFollowsClick", ref ffb) &&
+                    currentNode.TryGetValue("universalClickBlocking", ref ucb))
+                {
+                    if (ffb == focusFollowsClick && ucb == universalClickBlocking)
+                        return;
+                }
+            }
+
             ConfigNode node = new ConfigNode();
             node.AddValue("focusFollowsClick", focusFollowsClick);
             node.AddValue("universalClickBlocking", universalClickBlocking);

GameData/000_ClickThroughBlocker/ClickThroughBlocker.version

@@ -10,7 +10,7 @@
     "MAJOR": 2,
     "MINOR": 1,
     "PATCH": 10,
-    "BUILD": 21
+    "BUILD": 22
   },
   "KSP_VERSION_MIN": {
     "MAJOR": 1,
@@ -19,7 +19,7 @@
   },
   "KSP_VERSION_MAX": {
     "MAJOR": 1,
-    "MINOR": 11,
-    "PATCH": 0
+    "MINOR": 12,
+    "PATCH": 99
   }
 }

GameData/000_ClickThroughBlocker/changelog.cfg

@@ -5,6 +5,18 @@ KERBALCHANGELOG
 	license = Lesser GPLv3
 	author = Linuxgurugamer
 
+ 	VERSION
+	{
+		version = 2.1.10.22
+		CHANGE
+		{
+			change = Updated version file to use github for version info
+			change = Copied webpage to README.md
+
+
+			type = update
+		}
+	}
  	VERSION
 	{
 		version = 2.1.10.21

changelog.cfg

@@ -5,6 +5,23 @@ KERBALCHANGELOG
 	license = Lesser GPLv3
 	author = Linuxgurugamer
 
+ 	Thanks to github user @chambm for this amazing patch:
+		Universal click-through block for IMGUI windows on PAW / uGUI
+		Only works if Harmony is installed
+	Added a check to prevent the global.cfg from begin rewritten every time game settings change
+
+
+ 	VERSION
+	{
+		version = 2.1.10.23
+		CHANGE
+		{
+			change =Universal click-through block for IMGUI windows on PAW / uGUI
+			change =Added a check to prevent the global.cfg from begin rewritten every time game settings change
+
+			type = update
+		}
+	}
  	VERSION
 	{
 		version = 2.1.10.22