If you're looking for complete Apache referer_log analysis, you will have to use your tools rather than what Google provides you. I think they are trying to provide you a distilled version of referrals which will provide a good but incomplete picture.
The answer to your question is in a blog post from Google:
The relevant passage is:
we're showing a "Displaying" number for Impressions and Clicks. This
number represents a total count of the data displayed in the Search
Queries table. The number in bold appearing just above it is a total
count of all queries including the "long tail" of queries which are
not displayed in the Search Queries table. When the "Displaying"
number is not visible, such as when you select a specific country from
the "All countries" drop-down menu, then the bold number is the total
count of the data displayed in the Search Queries table.