I was beating my day because the index was not being printed on the report.
Later, after a good number of search(es), I found that this is interesting feature of MikTex 2.9
The problem was solved by changing %bm to %tm in the MakeIndex option.
Here is what I did:
Go to build > Define Output Profiles (Alt+F7)
Change %bm to %tm in the MakeIndex option.
Probably same thing needs to happen with Bibtex (if problem persists).
I am really glad that you are finding it useful. Happy Texing!