Looking at the results for my own account, on en.Wikipedia, a number of pages are shown with an assessment of "Unknown", rather than "Disambig".
What these pages have in common is having the Disambiguation template inside the Banner shell template, for example on en:Talk:Spon Lane Branch:
{{WikiProject banner shell|
{{WikiProject Disambiguation |importance= }}
}}
https://en.wikipedia.org/wiki/Special:PageAssessments?project=Disambiguation&namespace=0 shows the problem is rather widespread. Some pages get a "class" of "disambig" (which is what XTools is going off of) while others do not. Apparently some of the WikiProject templates are not using en:Module:WikiProject banner, which is what does the storage for Extension:PageAssessments. Or, there's a bug in the module. @MSGJ might know how to resolve this.
We no longer rely on |class=disambig to classify disambiguation pages as these are detected automatically by using en:Module:Pagetype which checks for the existence of a disambiguation template on the page