Translation:She seemed to be attentive, but that was not a common thing.
It means "but that is not something that happens often".
So, she does not often pay attention.
I expect the Esperanto translation is easy to understand once you understand the English since the words are pretty much 1:1, but reply if you are unsure about that as well.
"afero" is "thing" or "matter".
I think part of the problem is that it's not a typical way one would express that sediment in English, so the wording feels really awkward. Maybe it's a normal way to say that in Esperanto, but I have a feeling there might be a little bit different translation into English that would be considered more natural. I at least found the sentence to be very odd, and I don't know anyone who would say it like that.
esti is not just estis with the -s dropped -- it's an entirely different form.
It's the infinitive -- the form you would look up in a dictionary and the form you use with other verbs.
In English esti is "be" or "to be".
estis is the past tense form of that word: "was, were".
ŝi ŝajnis esti = she seemed to be. (You can't say ŝi ŝajnis estis any more than you could say "she seemed was" or "she seemed to was".)