Well, I don't have my iPad yet but I know that the iPhone YouTube App has always been a lucky dip at best -going to the mobile page works better than the app!
Yeah, it pisses me off no end.
Also the fact that videos don't get marked as read, unless they're viewed on a computer, is another headache - although that's YouTube's fault.
I have this problem too. I know for a fact that all my subscriptions were displaying correctly when I got my new iPad about a month ago. Just last week, I noticed this problem as well. Maybe something's wrong on YouTube's servers?