Greetings -
It is possible that not sewing it with a walking foot is the problem, but that would depend on how puffy the batting is. Since this is a table runner, my guess is that the batting is relatively flat. If that is the case, a walking foot might have helped, but there might be a different problem as well.
It could be that the tension on your thread needs to be adjusted. If either the top or bobbin is way too tight, it could cause your project to get wrinkled.
Hope that helps!
Happy Quilting!
Penny Halgren
www.How-to-Quilt.com
www.ThequiltingCoach.com
P.S. This book from amazon.com might have an answer for you: The Quilting Answer Book: Solutions to Every Problem You'll Ever Face; Answers to Every Question You'll Ever Ask