Let me try to make some points that might clarify things:
1. Changes in the preferences and language files might not take effect immediately. for the language file, you should press the "test" button after the changes you make. In either case, closing the window helps register the change.
2. The language file determines what parts of the text match to what scope. In your case, this needs to change, because otherwise your commands \Subsection and \Subsubsection are not being understood as meta.section.latex. You could optionally catch them as some other scope of your own, and do other stuff to them, but my understanding is that you want them to behave like the uncapitalized commands.
3. The preferences file (called "symbol list" here, but that is not important) tells TM the following: a) take the things from the text that have scope meta.section.latex (This is what the scope selector being "text.latex meta.section.latex" does), and use those for the symbol list (that's what the "showInSymbolList=1" does. b) Before showing them, perform a transformation to them. In this case, the transformation desired has the effect of replacing the subsection/section etc parts by appropriately lengthed spaces, so that it shows nicely nested. For instance, the following text:
\section{1st section} \subsection{1st subsection} \subsection{2nd subsection} \subsubsection{1st subsubsection} \section{2nd section}
will show up in the symbols list as: 1st section 1st subsection 2nd subsection 1st subsubsection 2nd section
Notice the extra spaces. Due to some error in our part, the line with the subsubsection will actually have one of the sub's replaced by spaces, but in general this will work as described above.
This is all accomplished by the "symbolTransformation" lines.
So the change in the language file will in fact have the desired effect of adding these \Subsection lines to the symbol popup, but if you want them to look nice as above, you need to make the analogous change in the "symbol list" preferences file.
I hope this helps. Let me know if you are still having problems with it.
Haris