This is a strange one, but dts bundle doesn't resolve relative imports which have a comment immediately before them. Example:
Source:
/** imports */
import base = require('./base');
Output d.ts:
declare module '__tardijs/transform/timeSeries' {
/** imports */
import base = require('./base');
Without the comment:
declare module '__tardijs/transform/timeSeries' {
import base = require('__tardijs/transform/base');