I would check you have the latest version of WebEssentials 2012 installed, as there were some issues with module import code not generating in builds 1.8.*
Also, there's an oddity in TS where imports inside a module generate no code:
export module test {
import myMod = module("MyMod"); // Generates no JS output
var class = myMod.someClass;
}
But:
import myMod = module("MyMod"); // Outside the module. Generates JS as expected.
export module test {
var class = myMod.someClass;
}