The Google Index column displays the current amount of pages a domain has indexed in Google.  This is the same as searching for "" in Google.

If you see pages still indexed in Google and even ranking for keywords, this indicates the domain should not have penalty issues.

Also it would be a good idea to rebuild the currently indexed pages when settings up your domain.

The Domain Index count is gathered when the domain is first interted to the database.  Also Domain Index is only available for expired domains with TF greater than '1' and referring domains greater than '10'.  Or for Auction domains, where referring domains is greater than '5'.  The reason we use these minimum metrics is due to the cost of accessing this data.