Pages are in ATW, but site is not?

When I do a search for my site with "site:domain.com" (w/o quotes of course), I get a ton of hits (okay, only 12 thousand), which could close to all the pages on my site.

However, when I just search "http://domain.com" or "http://www.domain.com", then ATW says "No entries for [domain.com...] in our index."

Searching "+link.all:domain.com -site:domain.com" results in 180 hits, so ATW knows of pages linking to my site.

Does anybody know why this is?