It's possible the flagged words are using f-i ligatures so the spell check doesn't see them as "benefits" and "specific", it reads them as "bene#ts" and "speci#c".
Ligatures had crossed my mind, but when I zoomed in to the words, the letters didn't look like ligatures, and the output proof didn't show ligatures. After reading your post I retyped the words and the spell check didn't flag them—even though they looked the same as before. Then I realized that the Frutiger font may be the culprit. When I selected the text (after reverting the document so my retyping wasn't saved) and changed it to Garamond (sans serif), I could see the ligatures!
It might also have been the language. The settings in the prefs have nothing to do with the language assigned to text, only the choice of dictionary to be used for each language when more than one dictionary is available. Language itself is a character-level attribute assigned either as part of the style or by selecting a language from the dropdown in the Character panel or Control panel.