src/Pure/System/isabelle_system.scala

--- a/src/Pure/System/isabelle_system.scala	Wed Sep 30 21:32:44 2015 +0200
+++ b/src/Pure/System/isabelle_system.scala	Wed Sep 30 22:01:17 2015 +0200
@@ -69,6 +69,8 @@
           bootstrap_directory(cygwin_root, "CYGWIN_ROOT", "cygwin.root", "Cygwin root")
         else ""
 
+      if (Platform.is_windows) Cygwin.init(isabelle_root1, cygwin_root1)
+
       def set_cygwin_root()
       {
         if (Platform.is_windows)