I had the same problem when I first got my 204 sharpmaker. I was following the manufactures instructions on alternating sides. Then I read the following portion of a sharpening FAQ authored by Joe Talmadge.
"You grind one edge along the stone edge-first until a burr (aka "wire") is formed on the other side of the edge. You can feel the burr with your thumb, on the side of the edge opposite the stone. The presence of the burr means that the steel is thin enough at the top that it is folding over slightly, because the bevel you've just ground has reached the edge tip. If you stop before the burr is formed, then you have not ground all the way to the edge tip, and your knife will not be as sharp as it should be. The forming of the burr is critically important -- it is the only way to know for sure that you have sharpened far enough on that side. Once the burr is formed on one side, turn the knife over and repeat the process.
To re-cap, you've sharpened one side only until you felt a burr along the entire length of the opposite side, then you switched sides and repeated the process. I suggest you do not follow the directions that come with many sharpeners, of the form "Do 20 strokes on one side, then 20 strokes on the other". You go one side only until the burr is formed; if that takes 10 strokes or 50 strokes, you keep going until you get a burr, period. Only then do you flip the knife over and do the other side.
Having raised a burr, our job now is to progress to finer stones, in order to make the edge smoother and remove the burr. So now we run the blade along the stone from end to tip, this time alternating sides with each stroke. Switch to a finer stone, and then do it again."
For the entire sharpening FAQ go here.
http://www.balisongxtreme.com/baliplanet2/BasicTerms/shfaq.htm