With the latest major release of igraph for R (igraph 1.0.0), the function to calculate the Kamada Kawai layout was re-written from scratch. The new function (layout_with_kk) seems to produce very different results than the previous function (layout.kamada.kawai) on the same networks (around 4k nodes, 18k edges). Maybe it's a change in the default argument values, or maybe something else.
I'd like to access the old function to figure out what is happening.