The skip named "defskip" available in the menu Layout->Paragraph inserts a \medskip internally. So why is it listed separately?
Because "defskip" is short for "default skip", i.e. the default skip for the given document (see menu Layout/Documents)
This notation doesn't appear in the docs and I can't remember that I've see it before. But anyway it is confusing - when using defskip, I expect a different behaviour from medskip, because they are listed separately. (The user can classify medskip as skip between small- and bigskip, but he can't imagine something about defskip.) The dialog Layout/Documents also don't have a defskip for paragraph separation.
Have a look at
Layout > Document > (Document Setting) > Layout > Separation > Skip
in LyX 1.3.X
Michael