It would be because those apps haven't yet been updated to run on gingerbread. Likewise, there are some apps that won't run on froyo as well. Bobclock D3 is one of those that comes to mind. The poor people that are still stuck on 1.6 (hello devour users) can't see about half the apps in the market because they won't run on 1.6. Once those apps have been updated for gingerbread, you should be getting them back though =)