In case you haven't been noticing, the Big Daddy update is causing a lot of sites to have all of their pages, except the index page, go supplemental. There is a big thread over at WMW about it. If this problem is affecting you, before you panic too much, be sure to read DaveAtIFG's response (msg #123). It may or may not be the actual truth, but it is logical and level-headed. An excerpt of his post:
The key thing to remember is that BigDaddy is being deployed to resolve canonical problems. I suspect sites are going supplemental down to the home page to identify the canonical domain. Then the site is respidered and rebuilt in Google's index using "new infrastructure," revised code that better handles canonical issues.
People have even starting commenting on Cutt's blog, hoping to get a response from him about the problem, but so far, Google is being mum about it. I'll let you know if I hear anything concrete.
UPDATE: Googleguy has finally chimed in on the subject in the afore-mentioned thread (msg 160). He says:
I'm happy to ask someone to check this out. Please send an email to sesnyc06 [at] gmail.com with specific domains and the keyword "gonesupplemental". I have a theory about this, which I'm asking the crawl/index guys to check out, but I'll need 5-10 specific examples to check if my theory holds. If my guess is right, I'll try to get the crawl/index folks to get things back to the previous behavior.
So, if you are having this problem, follow those directions, and things may get solved.