We had a new site go live on August 23,2010 with just over 2000 pages as shown on the xml site map that was submitted on that same day. Within a few days we started to see some obscure pages starting to show in the index ie. register, site map, forget password, maps... but nothing with any real content. As of this writing, almost three weeks later, not even home pages shows. In fact, site:www.example.com is not even in the index.
Strange part is that WMT shows that 1343 pages are indexed. Same home page was indexed in Bing in 3 days after submitting.
Only clue is that crawl error page shows a 401 that was encountered on August 23. We had to open up the site for some testing for a few hours and Google some how found and got a taste. Password protection was soon removed.
Any ideas on where to start or what to do or not do?
Thanks!