" 
 ::Sorry I didn't reply sooner. There's isn't much I can do, though - the scripts are fine, but the data is bad. Here's a quote from  over at the disambiguation project:  
 ::: fixed a big bug in job queue code last week. Links to templates should be refreshed automatically now, although any jobs that were in the queue before the fix have probably been deleted. 
 ::If that's true, then there's a window of time where templates were edited, but the pages that transclude those templates were not (and apparently never will be) null edited to update WhatLinksHere among other things.  "