Glad that worked out for you. If you don't need the entry at a specific place in the win.ini file, that should be doable.
The echo command used in conjunction with double redirects (>>) will append lines to your INI file, and any ascii file, for that matter. Emphasis because a single redirect overwrites an entire file. For instance:
echo "New Entry" >> %systemroot%\win.ini
Will create a new line that simply says "New Entry" in the win.ini file. Now, I'd make a copy of your win.ini file before doing this just to be safe.
If you need the entry like halfway down the file, though, that's a little tricky, and may require a third party tool. This is generally a lot easier on Unix.