Becouse this problem is still actual even for TS 1.0 and WebEssentials for VS 2013 Update 3, check this solution here: http://icanmakethiswork.blogspot.com/2014/02/typescript-and-requirejs-keep-it-simple.html
Or shortly:
1) Open project file.
2) find this lines:
3)Insert this lines before:
amd
amd