diff --git a/Source/Core/DolphinWX/VideoConfigDiag.cpp b/Source/Core/DolphinWX/VideoConfigDiag.cpp
index 2718adb90e..08d2697514 100644
--- a/Source/Core/DolphinWX/VideoConfigDiag.cpp
+++ b/Source/Core/DolphinWX/VideoConfigDiag.cpp
@@ -321,7 +321,10 @@ VideoConfigDiag::VideoConfigDiag(wxWindow* parent, const std::string& title)
                                                   wxGetTranslation(StrToWxStr(title)))),
       vconfig(g_Config)
 {
-  vconfig.Refresh();
+  // We don't need to load the config if the core is running, since it would have been done
+  // at startup time already.
+  if (!Core::IsRunning())
+    vconfig.Refresh();
 
   Bind(wxEVT_UPDATE_UI, &VideoConfigDiag::OnUpdateUI, this);
 
diff --git a/Source/Core/VideoCommon/MainBase.cpp b/Source/Core/VideoCommon/MainBase.cpp
index 5f5ce785ef..179efdbd41 100644
--- a/Source/Core/VideoCommon/MainBase.cpp
+++ b/Source/Core/VideoCommon/MainBase.cpp
@@ -192,7 +192,6 @@ void VideoBackendBase::InitializeShared()
 
   g_Config.Refresh();
   g_Config.UpdateProjectionHack();
-  g_Config.VerifyValidity();
   UpdateActiveConfig();
 }
 
diff --git a/Source/Core/VideoCommon/VideoConfig.cpp b/Source/Core/VideoCommon/VideoConfig.cpp
index d4097e5669..f561f94d37 100644
--- a/Source/Core/VideoCommon/VideoConfig.cpp
+++ b/Source/Core/VideoCommon/VideoConfig.cpp
@@ -48,7 +48,12 @@ void VideoConfig::Refresh()
 {
   if (!s_has_registered_callback)
   {
-    Config::AddConfigChangedCallback([]() { g_Config.Refresh(); });
+    // There was a race condition between the video thread and the host thread here, if
+    // corrections need to be made by VerifyValidity(). Briefly, the config will contain
+    // invalid values. Instead, pause emulation first, which will flush the video thread,
+    // update the config and correct it, then resume emulation, after which the video
+    // thread will detect the config has changed and act accordingly.
+    Config::AddConfigChangedCallback([]() { Core::RunAsCPUThread([]() { g_Config.Refresh(); }); });
     s_has_registered_callback = true;
   }