I have the same problem in the latest build of KAS and KSP 1.4.1.
I spent about 20 minutes trying to attach a magnet on an EVA, pressing "R" it says it only has one attachment point -- which is apparently the flat side of the magnet, not the attachment point side.
Like you, I've found that the magnet can be attached properly in the VAB, unfortunately my build meant I couldn't attach it in the VAB and was hoping to use the EVA to attach it properly.