I'm working on an EPP GFG right now and I have the same issue sometimes. From what I can tell you with my experience, once you remove the cardstock, give the flower a good press, very, very little steam. If you cut your own hexies, the variations in them as you sew will compete with each other and cause the rippling that you're experiencing, and it will continue until you remove the cardstock. Once you do that, your flowers will lay flat.
If you're starting with the center hexie, then adding the next round, then the next round after that, you can combat the rippling a little by pressing after each round, even with the papers still in the flower. I remove the papers as a round is completed, then press the flower again, then keep sewing. It's an extra step, but it works.
What I can also say is that when I cut my hexies, I wasn't perfect, so when you're attaching the fabric to the papers, take a second, really look at your hexie and trim it if it's not right. I've found many of mine to be slightly wonky, so a quick trim has helped. Also make sure that you're sewing on the edge of the hexie paper, any variation to your sewing along with the possibility you're working with a slightly wonky paper is going to make them to not lie flat.