Revtex 4.1 multiple affiliations

Works for me. I am using

Document Class: revtex4-1 2010/07/25/20:33:00 4.1r 

which fixes a number of bugs in the affiliation code.

Testcase:

\documentclass[superscriptaddress]{revtex4-1}
\begin{document}
\author{J. T. Ripper}
\affiliation{Bethlem Royal Psychiatric Hospital}
\author{Bugs Bunny}
\affiliation{Looney Tunes}
\author{Daffy Duck}
\affiliation{Looney Tunes}
\affiliation{Warner Brothers}
\maketitle
\end{document}

Result: