You may or may not be getting a burr. If you're using the Magic Marker Trick in the right way, and you're taking the ink off the very edge, it seems likely you are. However, because you're sharpening both sides instead of sharpening one side at a time, you're making it very difficult to detect.
I think that swiping the entire length of the knife in one pass is one of the more difficult ways to hold an angle, and isn't something I ordinarily recommend to noobs.... However, one thing at a time. Let's start with learning how to create and detect a burr.
There are several different kinds of burrs. The easiest to feel are the "bending burr" which occurs as a result of impact, and the "deposit burr" which is a product of sharpening. The most difficult kind to detect is the "wire," also a result of sharpening.
Start by picturing the ideal cross section of the edge of a sharp knife as a V. The cross section of an edge with a wire would be a Y, and the cross section of an edge with a bending or deposit burr would be a y -- with the tail of the burr bent over; or in the case of a severe impact burr, it could bend over on itself in the shape of a J. Note that the capital Y wire is not bent over -- and that's why it's so much harder to detect.
There are a lot of good ways to feel for a burr. The two easiest ways for most people are the thumb drag and the thumb push.
Thumb dragging means drawing your thumb across the edge of the knife. You probably already do this already as a way of seeing if the knife is sharp. If you've never done this, I can describe in more detail in a follow up post. When you thumb drag a knife with a sharpening burr, one side will feel more aggressive than the other. The more aggressive side will be the one on which the burr wasn't developed.
Thus, if you want to know if you've developed a burr sharpening the right side of the knife, hold the knife with its edge up and thumb drag in multiple places along the edge on both sides of the knife. If the the left side feels more aggressive you're detecting what you hoped for.
The thumb push is actually simpler -- or at least it is if you have a long enough thumbnail. Hold the knife edge up. Put your thumbnail against the face of the knife on the side you didn't sharpen, and very gently push up. When your nail hits the edge you feel should the burr's bend snag it.
In your specific case it's quite possible you developed a burr but then straightened it out, so you couldn't feel it. Because you didn't "chase the burr" in such a way as to facilitate deburring, it would mean that you "pulled a wire." That isn't a good thing, but it's easy enough to deal with as we move on down the road.
Your next step is to sharpen the knife on one side only, while using the Magic Marker Trick, until you can feel the burr with thumb drags and thumb pushes. Once you can do that, we'll move on to chasing the burr; and then to deburring.
Edited by boar_d_laze - 4/3/13 at 5:30pm