Keeping this thread alive, Bri, have you ever done any clip repair? (I know, you're so good that you never go over!) I've noticed that when I apply the tool to a selection, more often than not the bottom sweep of the wave seems to be flattened off while the top sweep will get a noticeable "repair" for the same clipped area. Is that an Audition/CEP bug? Should I dump it in favor of something that works? (I know, just avoid overs like the plague. 
Never go over? Hah! Oh, I've done plenty of clip repairing in Audition/CEP. Sometimes it works, sometimes it doesn't. But I've not experienced the results you mention.
I've found to achieve good results I must start and stop the highlighted selection I'm repairing on zero-crossings, a single channel at a time. For light clipping, I've had good results repairing a sizeable chunk at a time. For heavier clipping, I've needed to zoom into each individual peak and repair each individually. Even that hasn't always worked, and I've sometimes had to re-draw the waveform, with mixed results.