Yup, the notification system has been updated a bit. As Yoon said, it's still SUPPOSED to take you to the first "new" episode, rather than the last read comic (that's a bug, and we'll fix it right away). If there aren't any "new" episodes, then it'll remember your last read comic just as it did before.
Besides the "new" tag showing instead of the number of new episodes per series, there are a few other updates:
The currently selected episode is more obviously marked, with colored text (or a border around the thumbnail when you collapse the sidebar)
Episodes you have read now turn slightly transparent on the list, while unread episodes appear fully bright / opaque. Now if you're jumping around or don't remember where you left off in a series, you can quickly find which episodes you haven't seen yet.
New episodes are marked as "new" the first time you see them after they're added, to distinguish the episodes that were just added from one that were already there, but which you might not have read yet.
Hope that clarifies things a bit! Brian's post will have more details.
