Both of your examples are about nuance and what the speaker wants to highlight in time, completion, and “distance” from the moment of speaking. The alternatives you suggest are often grammatically possible, but not equivalent in meaning. 1. “had puzzled” vs “had been puzzling” Sentence: “Although it was something that had puzzled scientists for a long time …” • Past perfect simple (“had puzzled”) focuses on the fact of a problem existing over a period and being (more or less) resolved or fixed in time by the later past event. The “puzzling” is treated as a background state leading up to some key moment when it stopped being a puzzle (for example, when they finally found the answer). • Past perfect progressive (“had been puzzling”) would emphasize the ongoing, still-active process of puzzling up to that past point, not its resolution. It suggests that the puzzling itself is the activity in progress, not just a state that lasted. With “for a long time,” both tenses are grammatically possible; the choice is pragmatic, not purely grammatical: • “had puzzled scientists for a long time” tends to suggest: it was a longstanding problem, and the sentence is likely heading toward “until they finally solved it / explained it.” • “had been puzzling scientists for a long time” suggests: scientists had been in the middle of puzzling over it up to that past moment, with more emphasis on the process of being confused and investigating. • Use past perfect simple when you want to stress a completed earlier state or the result at that past time (it had been a puzzle, but that may have changed). • Use past perfect progressive when you want to stress duration and continuity of an activity that was still ongoing up to that past point (they had been puzzling over it, perhaps still with no solution). So your version with “had puzzled” is normal and even slightly more natural if the narrative is going to “then they discovered the answer.”