Kodachrome has a "bas relief" effect on the emulsion surface.
It is quite noticeable if you hold the slide at a obligue angle when viewing the emulsion surface.
I use a Nikon CS9000 scanner and I have found focus to be a problem when using the dedicated slide tray.

The problem seems to be solved by removing the slide from the it's holder and using Nikons FH869GR glass holder.