I had that problem when I was using a Linksys router and Comcast (cable company for those unfamiliar) cable modem internet. Now I have Verizon FiOS and its complimentary router (Actiontec brand, I believe) and haven't had that problem. Not sure if the problem was due to the Linksys router or internet provider.
The notification system is exciting, and I know that this is the first beta release, but I think it could be improved. Currently, the system seems to work like that for personal messages. You are taken to a list of notifications, and clicking on one opens a new page with more details. Personally, I think something more lightweight and less complex would be even better. Something similar to the way Facebook displays notifications would be nice. For example, instead of seeing a list of:
New reply to your status Today, 02:12 PM
New reply to your status Today, 11:07 AM
New reply to your status Today, 10:58 AM
And then having to click on each one to see the pertinent details on a new page for each, just list the details of the notifications:
Bartosz Misiak replied to Mike54's status | Today, 02:12 PM iikato repled to AnthonyKinson's status | Today, 11:07 AM
You could have an AJAX button/check mark/etc. next to each notification that allows a user to mark each one as read/unread. I think that, in general, this way is simpler and gives more information at one glance without having to click into additional pages.
There also needs to be a more visible way of knowing that you have new notifications. For example, like the number that shows up over the profile picture in the user navigation when you have a new private conversation.