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I have a table that I have attempted to set up as follows (contrived example):

% Preview source code



%% LyX 2.3.2-2 created this file.  For more info, see http://www.lyx.org/.

%% Do not edit unless you really know what you are doing.

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}



makeatletter



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.

%% Because html converters don't know tabularnewline

providecommand{tabularnewline}{\}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.

usepackage[table]{xcolor} %for use in color links

usepackage{colortbl}



makeatother



usepackage{babel}

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 & Headertabularnewline

multirow{8}{*}{cellcolor{white}rotatebox{90}{Lorem ipsum}} & Content & ### & ### & ### & ### & ###tabularnewline

 & Content & ### & ### & ### & ### & ###tabularnewline

 & Content & ### & ### & ### & ### & ###tabularnewline

 & Content & ### & ### & ### & ### & ###tabularnewline

 & Content & ### & ### & ### & ### & ###tabularnewline

 & Content & ### & ### & ### & ### & ###tabularnewline

 & Content & ### & ### & ### & ### & ###tabularnewline

 & Content & ### & ### & ### & ### & ###tabularnewline

end{tabular}rowcolors{2}{}{}

parend{flushleft}

end{document}

Apologies in advance for this being generated code, but a commenter below asked for a complete compilable example instead of just the tabular snippet that I had had originally posted. Hopefully this will make it clearer, but I apologize in advance if it has obfuscated the problem.

Anyways, this renders as:

As seen, the sideways header that I am using on the left side of the table gets overwritten by the color of the row, interrupting the text.

What I would like to do is have that entire first column containing the left row header be white on all rows, which I tried to do by adding cellcolor{white} to the multirow cell, but as the image indicates, it only cleared the top gray strip in that cell, and didn't do anything to the rest of the first column.

How can I get the full text of the header to show up correctly?

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 ipsumhspace{2dimexprhtstrutbox+dpstrutbox}}

end{tabular}%

rowcolors{3}{gray!20}{}%

begin{tabular}{cccccc}

 & multicolumn{5}{c}{Lorem ipsum dolor sit amet}tabularnewline

 & Header & Header & Header & Header & Headertabularnewline

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 noindentbegin{flushleft} is nonsense, because it just adds unwanted vertical space (a blank line). Also parend{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 & Headertabularnewline

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}

parend{flushleft}

end{document}