I'm still having issues with the .ini reverting after passing through the launcher. I'm applying the mouse acceleration changes, all my other changes appear to have stayed.

Yes it's because the launcher(due to steam) is over writing the updated preferences file, with the default one.

You can try this, basically it shows you how to make a batch file to bypass the launcher, and hopefully not have your settings revert repeatedly.
http://newvegasnexus.com/downloads/file.php?id=34935