Your internal linking is pointing back to /index.php for starters. This is a different url to www.47lab.com/ This means that any links pointing into subpages aren't passing PR back to the root. Quite why it makes such a massive difference in your case I don't know. Both the root and index.php are PR1. I would have expected one of those to be a PR3 (or something like that) with the internals being PR5. Fix the internal linking problem to start with, you might need to wait until the next update before knowing whether that fixes the problem. I've had similar on one of my sites, but in my case I have some pages still pointing to /index.php, IBL's pointing to / and the non www existed as well. Fixed them all and the root went to at least the same as the internal pages at the next update - it was a little embarassing at the time.
I have the same problem aswell my internal pages are PR4 and PR3 but the index has no PR. the Site is http://www.bloggerteam.com Other sites doing well the PR effect only hit this site. No idea about it aswell.
Well, it seems that my site went from PR0 to PR5. Seems as if a 301 re-direct does indeed pass pagerank. Wohoo! It's just a pity that I've lost most of my keywords I've been starting to rank in Google for again. Oh well...
I have been trying to get more info about this in another thread, but of late it's off topic, all about adsense at current. I have the same problem, and it is inexplicable. I went from 3 > 5, most of my other pages are a 4. In my webmaster resources directory, the pages are 3's or 4's, with one 6 standing out...
I saw a few sites that I planned to buy links from jump from PR6 to PR 4 so google is doing a good job of penalizing link sellers. Is anyone getting any more traffic?That's what's important.
Ok, the point is that all my BL are pointing to the www.47lab.com and none to internal pages (except sitemap and index page), but why the heck do internals get a better PR from an index page of PR1 and the index page gets a looser's PR1 from 600 backlinks in google?
That is caused by the internal linking structure for you site. Forget about whether links are not shown in google or not.
Ohhhh, okay...wait a minute. since when english is India's primary Language??? Anyway welcome to double redded club, I hope you'll enjoy the company of Gaydood and IamNerd.