1

What is the difference between this sentences?

I had said no, because I was in the middle of getting Windows NT shipped, and because Microsoft had been generous with stock options.

I had said no, because I was in the middle of getting Windows NT shipped, and because Microsoft was generous with stock options.

2

They read nearly the same to me without additional context.

Had been indicates an ongoing state in the past, and that that state ended in the past as well. In this particular case, the narrator is saying that Microsoft's generosity was an ongoing state in the past at least up to the time the narrator is describing (when he or she said no). No information is conveyed about Microsoft after this time.

Was indicates that something took place definitively in the past: Microsoft's generosity took place in the past, with no information about exactly when in the past that was true. In this case that could define the time up until the narrator said no, or even up until the present (when the narrator is relating this story about the time he or she said no).

In typical use (in the United States, at least) I don't think that anyone would interpret the sentences as having different meanings from one another.

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