Got the okay from Nathan to commit this: It's a small patch for Win32 Ghost that prevents a Blender window from setting the cursor position when it's not the active window.

intern/ghost/intern/GHOST_SystemWin32.cpp

@@ -271,6 +271,8 @@ GHOST_TSuccess GHOST_SystemWin32::getCursorPosition(GHOST_TInt32& x, GHOST_TInt3
 
 GHOST_TSuccess GHOST_SystemWin32::setCursorPosition(GHOST_TInt32 x, GHOST_TInt32 y)
 {
+	if (!GetActiveWindow())
+		return GHOST_kFailure;
 	return ::SetCursorPos(x, y) == TRUE ? GHOST_kSuccess : GHOST_kFailure;
 }