Does your preferred shelf configuration use the "Shrink to content width" option?
If I don't use the "Shrink to content width", the shelf seems to take up the whole side of the screen, and the position configuration loses granularity (selecting a position in the corners or the middle of a side results in the same shelf position).
Also, it's the default option for a new shelf, so I generally leave it as is.
Both my shelves do, and I suspect the third one I used to have long ago did as well. In my case, they are both on the bottom, one left, one right, and they have to be different vertical sizes. For whatever that's worth.