It's kind of hard to picture what you're describing. If it was flat when you stitched it and nothing shifted, then it should lie mostly flat when you turn it....you're sure you caught the batting and it's not bunched up inside???
Whenever i use this method, i always stitch all the way around the perimeter after i turn it right side out - from 1/2 - 1" depending on the quilt. This makes a kind of false binding and keeps the edges from shifting.
Sorry...guess i wasn't much help.