To identify Government documents, Query collections search using the material format index (i.e mt:gpb). Collection Evaluation determines the count using the call number subject division in the OCLC Conspectus. So if a title does not have "GOVDOC" in the 050 tag, it will not be picked up as a Government document in Collection Evaluation. This often causes the number in Collection Evaluation to be lower than that of Query collections searching by material format.
There is more on the material type index and what qualifies for each type.