This puzzles me as well. And is kind of a deal breaker for me as I make more use of YouTube's subscriptions than anything else.

I've had a similar experience with YouTube being rather unwatchable. The solution that Kris mentioned above worked for me only temporarily. But I found another solution that's currently working (for now). I blogged about it here: http://mlmjr.com/blog/michaels-…

Feedly has this option. By default it's set to automatically mark-as-read entries in "Full Article" inlined view. But you can change it to all views in the preferences.