Hi John, A couple of things. First, you have included the knitr and short-inset-names modules in the document, which as far as I can tell are not used for this minimal example. I removed them since I'm not yet set up to work with those. This shouldn't cause any problems, but I thought I'd mention it in case.
As a disclaimer, I am not exactly sure what I'm doing, but when I opened up the apa.cls file and searched for paragraph and subparagraph, I found: \renewcommand{\paragraph}{\@startsection{paragraph}{4}{\parindent}% {0\baselineskip \@plus 0.2ex \@minus 0.2ex}% {-1em}% {\normalfont\normalsize\bfseries\itshape\addperi}} \renewcommand{\subparagraph}[1]{\@startsection{subparagraph}{5}{1em}% {0\baselineskip \@plus 0.2ex \@minus 0.2ex}% {-\z@\relax}% {\normalfont\normalsize\itshape\hspace{\parindent}{#1}\textit{.}}{\relax}} The thing is, with the document you sent, the paragraph part is working, but the subparagraph part is not. So, if we use a little trial-and-error to put them together, I end up with the following, which seems to work if you paste it into your preamble (under Document->Settings->LaTeX Preamble). \renewcommand{\subparagraph}{\@startsection{subparagraph}{5}{\parindent}% {0\baselineskip \@plus 0.2ex \@minus 0.2ex}% {-1em}% {\normalfont\normalsize\itshape\addperi}} As a disclaimer, I'm not actually sure what I've done there, and it could break something else, but it seems to work for me...maybe somebody who understands things better can provide more insight. I hope this helps. Jacob