The first sentence expresses that she lived/studied/worked there for two years ' not exactly until/long before ' he showed up. The second sentence expresses that she continued to live/study/work there for two years ' until/right before ' he showed up.
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AnonymousI think the following sentences with the past perfect and past perfect continuous mean the same.That's pretty much true, but the emphasis is different. The first focuses on two years of time as a block of time; the second focuses on two years of activity.