On Windows, the layout file is with UNIX EOL. I believe the fix should be trivial. See below in Git Extensions diff format. I can also provide it as a pull request at https://github.com/doxygen/doxygen. Let me know.

Thanks,
Georges

diff --git a/src/layout.cpp b/src/layout.cpp
index 01d5d18..1d778a6 100644
--- a/src/layout.cpp
+++ b/src/layout.cpp
@@ -1396,7 +1396,7 @@ void LayoutDocManager::parse(QTextStream &t,const char *fileName)
 void writeDefaultLayoutFile(const char *fileName)
 {
   QFile f(fileName);
-  if (!f.open(IO_WriteOnly))
+  if (!f.open(IO_WriteOnly | QIODevice::Text))
   {
     err("Failed to open file %s for writing!\n",fileName);
     return;