\newpage stays in right column

I had the same problem with IEEE, but in my case, I used

\clearpage

instead of

\newpage

That's it.

I don't quite understand what causes the problem, but apparently it has something to do with the fact that your text is a single line which cannot be accomodated in two columns, and somehow TeX decides that, since it has to go in a single column, better to the right.

As soon as you add a second line to that page, the problem vanishes (although the result is far from optimal, imho:

\documentclass[aps,prb,reprint]{revtex4-1}
\usepackage{lipsum}
\makeatletter
\newcommand*{\balancecolsandclearpage}{%
  \close@column@grid
  \cleardoublepage
  \twocolumngrid
}
\makeatother
\begin{document}
\lipsum[1-4]
\balancecolsandclearpage

This text is in the right column. But I added more text so that at least two 
lines are required.
\end{document}

The problem gets solved if you put a \clearpage after the contents of the last page:

\documentclass[aps,prb,reprint]{revtex4-1}
\usepackage{lipsum}
\makeatletter
\newcommand*{\balancecolsandclearpage}{%
  \close@column@grid
  \cleardoublepage
  \twocolumngrid
}
\makeatother
\begin{document}
\lipsum[1-4]
\balancecolsandclearpage

This text is in the right column. But I added more text so that at least two 
lines are required.
\clearpage
\end{document}

It also works when there is a single line, like in your original question. Perhaps it could be a good idea to put \AtEndDocument{\clearpage} in your preamble.

I couldn't find a good solution for RevTeX in two column mode, I did this in the past but it might not work all the time (it depends on which column you are it).

\maketitle
~
\newpage
~
\newpage
...