Sivaram,
I'm sorry it doesn't work for you. It's been tested on hundreds of files here, but may be missing something that's in your code.
First, I would like you to verify you're looking at the new files created. They will be in the same directory as the original, but will be name like this:
@PATH\@NAME.ReIndented.sql
If it's not too much, please send one or more of the files that don't work to me at dtecmeister at gmail.com and I can improve the tool to include the code situation you have.
Thanks,
Jeff