In spite of earlier announcements, Hadley continues to move ggplot2 forward, read more here:

Since I´ve done my last 20 papers or so with ggplot, I immediately adopted the latest version for papers in preparation and noted slight differences in my graphs. After a little hunting I solved the problems, this might speed up your own search:

+  theme(axis.title.y = element_text(hjust = 1, margin = margin(r = 7)), axis.title.x = element_text(hjust = 1, margin = margin(t = 7)))

Let ggplot rock on, enjoy!