One or more of the apps you are updating is seeing that you have not yet gone to ios5. All the iwork app changes, for example, will not upgrade until you do. What you can do is tick them individually. If that particular app will update, then it will. If it won't it will tell you, and you can go back and get them later after you do the ious 5 update. Last night i decided to update before i started the ios 5 upgrade, and there were 16 apps waiting for up date. All but 5 did update, but not the i works, and 2 others.
It takes a little longer to do them 1 at a time, but it is better than staring at the stupid 'not eligable' notice.