I just pushed an update that changes the layout of the notifications section to something that should be significantly easier to navigate (and after we've seen it work well for a few days, we will also add a small number next to the bell-icon that tells you how many unread notifications you have).
I've also fixed the private messaging system to now be functional, though still horrible on many dimensions. But at least people should now get notifications if you send them messages, and actually be able to see your messages.
I've also fixed a bunch of bugs that caused comments to appear on the wrong post. Sorry for anyone who was affected by that.
Let us know if you run into any problems, this was a pretty major update behind the scenes, so there is a higher than normal chance that something broke somewhere.