I just found out how to save a couple of frustrating hours trying to track down why font encodings don’t seem to work in LaTeX when using Sweave. Somewhere along the line, it looks like ae.sty is getting directly or indirectly invoked by Sweave, which means that any font encoding directives placed before usepackage Sweave will be ignored. The solution is to declare the Sweave package import like so:
\usepackage[noae]{Sweave}
And fonts should work as specified.