There was a global option fig.show
set in the first chunk:
opts_chunk$set(fig.show='hold')
And that option is critical here. You may see a simpler example here. Alternatively, you can use it as a local option:
<<two-high, fig.width=3, fig.height=2.5, fig.show='hold', out.width='0.49\\linewidth'>>=
plot(cars)
boxplot(cars$dist,xlab='dist')
@