When searching within the filters, results are only returned for values that do not appear in the first five items OR the additional items that appear when selecting "Show More". If a department shows in the filter or by clicking Show More, the search box will not turn up results for this department if you search. 

We do have a request in our portal here regarding this behavior as well! https://blackbaudk12.ideas.aha.io/ideas/K12CO-I-1386