A few clients have experienced an issue where their workflows trigger was dependant on the status field that DocGeneration creates in the initiation list from SharePoint for the template that is being merged.
What we propose, is to find out what the timer job service is set to for WAS on the SharePoint server (should WAS be in use). This timer set in CA will be the maximum amount of time it will take to convert the document after merge (example it will run every 20 minutes in batches for SharePoint 2010). Therefore you should set your delay timer on the workflow for at least 15 seconds longer than that of the WAS job timer service.
By delaying the timer, it will give SharePoint time to update the status field successfully (that the workflow is checking for initiation purposes) before the workflow reads the status field of the merged item from the SharePoint list.
The template in the Template Gallery:
The list item in the Custom SharePoint list showing the status field the workflow is based on: