Caffeine is still in the experimental stages, which means it is probably only being updated whenever they make code changes. If they made a change to the main algorithm that filtered out your site, they may not yet have made the same change to Caffeine.
Use the site query command to see if your site is still in Google's main index. If it is not, the site is in trouble. It may still be in trouble when Caffeine is merged with the main algorithms. Caffeine is mostly an infrastructure re-write to speed up searches, but there are some ranking algorithms changes, as well.
I have not seen an announcement about when they are going to flip over to the the Caffeine algorithms. They probably will not tell us when they do.
"Democracy is two wolves and a lamb voting on what to have for lunch. Liberty is a well-armed lamb contesting the vote." -- Benjamin Franklin