Site Index is Dropping..

This is really getting me frustrated ..

I install upgrade from RC1 to Gold version (3.3.0) and my indexes drop from 500 to 300, I had my url set as no www, after I installed vBSEO I changed it with www, but I don't think this is the cause because when I searched google using the site: command, I searched my site with www and apparantly it didn't raise, as a matter of fact when I searched it with out www, the index dropped.

vBSEO is useless?

It can fluctuate. I know google just did a pr update that could have something to do with it.

My site went from 40k or 50k to 18k and then back to like 20k...

And how has your traffic from search engines changed over this period ?
(check Google Analytics, if you use it)

More indexed pages doesn't necessarily mean more traffic.
I'd prefer 200 pages in index that bring 1K visits instead of 500 pages that bring nothing.

just post content on your website, sign up for the site map in Google webmasters and analytic LEAVE IT. Dont change URL structures unless you really have to. As you can see in the vbseo panel, URL Structures are called "Set it and forget it" for a reason

If you keep changing things it will never settle. leave your settings alone for a while and track your search engine referrals with an analytics tool, not the site: command.