This MWE

\documentclass[12pt]{report}%
\usepackage[T1]{fontenc}
\usepackage{fancybox,fancyvrb}
\usepackage{times}
\begin{document}
\begin{Verbatim}
htlatex foo.tex "htm,3"
\end{Verbatim}
\end{document}

when compiled using htlatex foo.tex changes the " to tilde.

Please see

http://tex.stackexchange.com/questions/220908/why-quotes-in-verbatime-become-tilde-when-adding-usepackaget1fontenc-with

For pictures showing the results.

Using texlive 2014

File List
report.cls 2014/09/29 v1.4h Standard LaTeX document class
size12.clo 2014/09/29 v1.4h Standard LaTeX file (size option)
fontenc.sty
t1enc.def 2005/09/27 v1.99g Standard LaTeX file
fancybox.sty 2010/05/15 1.4
fancyvrb.sty 2008/02/07
keyval.sty 2014/10/28 v1.15 key=value parser (DPC)
times.sty 2005/04/12 PSNFSS-v9.2a (SPQR)
t1ptm.fd 2001/06/04 font definitions for T1/ptm.
t1pcr.fd 2001/06/04 font definitions for T1/pcr.
***********

The problem goes away when commenting the times package or the fontenc package.