Lukas,
How are you measuring how perpindicular the blade is? This si something that I have struggled with. Because to the taper on most knives and the difficulty in getting a square positioned as a reference, and the inability to even hold an angle cube on both sides in the same way repeatedly, I have no clue on how to do this properly. So, what are you using to make the determination that there is a degree difference?
Have you looked at this:
http://www.wickededgeusa.com/index.php?option=com_content&view=article&id=78:can-the-wicked-edge-sharpen-fully-flat-ground-blades&catid=31:general&Itemid=46
Or this:
http://wickededgeusa.com/index.php?option=com_kunena&func=view&catid=6&id=1244&Itemid=63
I was looking for a video online that shows well why the angle marks on the moveable side will always be a bit different (on the right side) than the left because one side is fixed and the other moves. I could not find it, but it inuitively makes sense and the reason can be proven with simple geometry.
Are you using an agle cube or similar to measure angles? If so, get the knife as close to perpindicular as you can, set your angles equally and you should be good. Even without the angle cube, you can adjust the angles (not neccessarily to the same place on the bar on each side), to get an even bevel side to side and you will get a wonderful edge.
I have found that with using some of the tips discussed here, and paying attention to the details. I can get a blade mounted up well enough to sharpen it with no noticeable difference between the bevels on each side. In the end, I have found that even if there is a degree difference from side to side, it does not significantly affect the sharpness that can be achieved, nor the handling of the knife while cutting.
Phil