Jennifer,
We had a pretty similar experience with Daphne. As soon as she was home after the surgeries, she was soooo happy, and so energetic, and we thought the surgery had been a true miracle. Then some of her old issues started creeping back, mainly fussiness and migrain-type episodes. They were better than before, but the surgery hadn't completely eradicated them, as we had started getting our hopes up for.
Those issues have gradually improved, and we still deal with them once in awhile (Daphne had an indirect bypass). We still think her surgery was a true miracle, though

She is generally so much happier, so much more interactive, and so much stronger than she was before surgery. And, best of all, she's had no more strokes, or stroke-like incidences, which is really what the surgery was for.
Jenny