Hi Akshay,
First, let me say that I normally minimize CSS and Javascript using:
and both seem to work fine.
Also, it's not really necessary, or even a good idea, to combine all JS files into one big JS minimize file for a number of reasons.
It is not good to "over optimize" and little really great comes of it, in my view.
Most sites like this are changing often and there is always a lot of Javascript code to write, modify, change and debug. Creating "mothers of all minimized Javascript files" make things "a nightmare" and it is better to smartly combine them, and that cannot be done by tool because we need to know that we are developing, where the issues are, what is changing, and what is static.
But anyway, I'm not focused on it and it is not on the site development critical path to worry about minimizing more JS and CSS. I have a lot more important functional code to write for the next month or so.
Cheers and Thanks!