Ok, here's the clean snippet.

 The dispersion studies above have all used 
\begin_inset Formula $D=D_{\textrm{mol}}$
\end_inset 

, the species' coefficient of molecular diffusion.

Note no space before final $ and no space on next line before the comma.

Read it in, write it out:

 The dispersion studies above have all used 
\begin_inset Formula $D=D_{\textrm{mol}} $
\end_inset 

 , the species' coefficient of molecular diffusion.

Note spaces both before final $ and before comma

If, I edit the stuff in lyx before writing anything, then I get:

 The dispersion studies above have all used 
\begin_inset Formula $D=D_{\textrm{mol}} $
\end_inset 

, the species' coefficient of molecular diffusion.

Ie, the space before the $ is still there but the one before the comma has 
not reappeared.

If I open, save, close several times, doing nothing else to the document

 The dispersion studies above have all used 
\begin_inset Formula $D=D_{\textrm{mol}} $
\end_inset 

   , the species' coefficient of molecular diffusion.

So it appears that the problem really lies in what you do after the 
\end_inset command.

Angus

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