My symptoms improved on prednisone, but I was by no means back to normal. I don't know if there was still inflamation, but I did wonder whether some of my digestive symptoms were not due to Crohn's. I've been diagnosed with delayed stomach emptying, and have had some problems with my rectum that are unrelated to Crohn's, so I figured even if I wasn't flaring, I'm never going to have good digestion.
It is possible that prednisone hasn't got your Crohn's completely under control, but another possibility may be digestive problems from a different cause. I find it very hard to determine which symptoms are due to which problem sometimes!