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?