This issue is now solved in Chutzpah 2.4.
Chutzpah Specific Reference
With the addition of TypeScript support a few releases ago several people reported issues when using Chutzpah with the TypeScript plugin in VS. The problem occurs since both TypeScript and Chutzpah are using the comments for different purposes. To get around this issue Chutzpah now supports two ways to reference dependent files.
The existing general way
/// <reference path="foo.js" />
The new Chutzpah specific way
/// <chutzpah_reference path="foo.js" />
Using the latter will let Chutzpah know about your dependency graph and should not confuse the TypeScript compiler.