library(ggplot2)
library(cowplot)
data(diamonds)

#Everything works well
p1 <- ggplot(data=diamonds) + geom_point(aes(x=x,y=y))
p2 <- ggplot(data=diamonds) + geom_point(aes(x=x,y=z))
plot_grid(p1,p2)

#Rotate axis labels
theme_update(axis.text.x=element_text(angle=90,hjust=1))
#Breaks plot_grid
plot_grid(p1,p2)
#Actually breaks all of cowplot since ggdraw() doesn't work anymore
ggdraw()

#Can be "restored" but create other bugs
theme_update(axis.text.x=element_text(angle=90,hjust=1,debug=FALSE))
#Now, we have axes around the grid with rotated "axis labels" (actually the coordinates of the grid)
plot_grid(p1,p2)

#A workaround is to define only for the plots
#Restore the theme
theme_set(theme_cowplot())
#Define the settings of the theme "locally"
plot_grid(p1 + theme(axis.text.x=element_text(angle=90,hjust=1)), p2 + theme(axis.text.x=element_text(angle=90,hjust=1)))