Maybe more to it than that. The first appraisal might have been done subject to the rehab, and the rehab was ultimately not as high-end as what the original appraiser assumed it would be.
Nobody will be able to tell you what the discrepancy is unless you post pics of your rehab, along with specs, along with address of the comps from each appraisal. I wouldn't be demanding a second appraisal until I fully understood both, which I doubt you do given the line of questioning that brought you here. No offense.