Well, Pages by themselves are not really different - just the way how they are stored in the database.
This can cause issues with plugins that are querying posts in the old way (based on the older versions DB structure), or with custom query strings - e.g. if your theme is using something else than the default Loop.
I just wrote a brief article with some illustrations to show what has been changed in the database. I hope it will be helpful, at least to understand why your Pages show up among posts :) - or disapppear.