Specifying a starting column with colortbl package and xcolor

Using \multirow is the cause of your troubles.

\documentclass{article}
\usepackage{graphicx}
\usepackage[table]{xcolor} %for use in color links

\begin{document}

\begin{flushleft}
\begin{tabular}{@{}c}
\rotatebox[origin=c]{90}{Lorem ipsum\hspace{2\dimexpr\ht\strutbox+\dp\strutbox}}
\end{tabular}%
\rowcolors{3}{gray!20}{}%
\begin{tabular}{cccccc}
 & \multicolumn{5}{c}{Lorem ipsum dolor sit amet}\tabularnewline
 & Header & Header & Header & Header & Header\tabularnewline
Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
\end{tabular}\rowcolors{2}{}{}
\end{flushleft}

\end{document}

I have reduced the document to the minimum necessary.

Note that \noindent\begin{flushleft} is nonsense, because it just adds unwanted vertical space (a blank line). Also \par\end{flushleft} is not necessary.

What does the strange \hspace command? It adds the vertical size of the two header rows.

In the following code, I have added a \cellcolor{white} command to all the cells that are in a gray row and should actually have a white background. I have also shifted the \multirow command from the first row to the last row and used -8 instead of 8:

\documentclass[english]{article}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\usepackage{geometry}
\geometry{verbose,tmargin=0.25in,bmargin=0.25cm,lmargin=0.25cm,rmargin=0.25cm}
\usepackage{array}
\usepackage{multirow}
\usepackage{graphicx}

\usepackage[table]{xcolor}


\begin{document}
\noindent 
\begin{flushleft}
\rowcolors{3}{gray!20}{}%
\begin{tabular}{ccccccc}
 &  & \multicolumn{5}{c}{Lorem ipsum dolor sit amet}\tabularnewline
 &  & Header & Header & Header & Header & Header\tabularnewline
\cellcolor{white} & Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
 & Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
\cellcolor{white} & Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
 & Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
\cellcolor{white} & Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
 & Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
\cellcolor{white} & Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
\multirow{-8}{*}{\rotatebox{90}{Lorem ipsum}} & Content & \#\#\# & \#\#\# & \#\#\# & \#\#\# & \#\#\#\tabularnewline
\end{tabular}
\par\end{flushleft}
\end{document}