I have one chip out of the edge of one of my medium rods too. I've smoothed it out some by rubbing the edges of the other rod against it (kinda like rubbing two sticks together). This has helped, but usually I just avoid using that side now. To tell you the truth, I rarely go beyond the medium rods on edge anymore. I like the toothy edge they give the blade, and they'll shave hair.
I have a set of ceramic crock sticks in a similar (but wooden block) type of arrangement. They measure out at a ~56 deg angle. After sharpening on the Sharpmaker at 40 deg, I just swipe on the larger angled crock sticks 5 or 6 times each side lightly to remove the wire edge, and I'm done. The same thing could be done on the Sharpmaker by inserting the fine rods on edge, and tilting the knife slightly.
The only real trouble I've had with sharpening knives on the Sharpmaker is many knives need to be reprofiled to a thinner edge first, before the Sharpmaker will work. Some of the knives I've sharpened need a substantial amount of material removed. This seems to be particularly true with the thicker, military style knives such as KaBars, jet pilot survival knives (Camillus and Ontario), Cold Steel's stuff- an SRK comes to mind, an Anza Bodington, and knives like that. I even had a Randall Model 18 that needed reprofiling first. Like I said above, for reprofiling I use a GATCO coarse diamond stone. Its alot faster than the Sharpmaker.