I would like to change the theme that ggplot uses, but I am having difficulty understanding the theme_update()
documentation and examples.
I don't know why this works, but it does. Just insert the line theme_set(newtheme)
before you call align.plots.
It could be considered a bug in ggExtra::align.plots(). This function computes the size of different elements of a ggplot, such as y-axis label and legend, and aligns the plots accordingly to have the plot panels on top of each other. If you set your theme to use theme_blank() for some of those graphical elements, the function gets confused as the underlying grob (ggplot2:::.zeroGrob) isn't quite like other grobs.
While it might be fixable (*), I think you'd be better off considering other options:
use a dummy facetting variable to have ggplot2 automatically align the two panels
use gridExtra::grid.arrange() or plain grid viewports to have the two plots on top of each other; since you removed the elements that may offset the plot positions, there should be no problem.
(*): now fixed, try
source("http://ggextra.googlecode.com/svn/trunk/R/align.r")