Im unsure about how to fix your problem but I prefer to try to have all my scripts in a certain language rather than multiple languages as when it comes to compile time I know I will not have any errors such as this. There is a Javascript to C# Converter around by Leepo http://m2h.nl/files/js_to_c.php , There is also a much more advanced better version being sold on Unity Asset Store. Just my Opinion though, do what you want.
Script Compiling Reference http://unity3d.com/support/documentation/ScriptReference/index.Script_compilation_28Advanced29.html