Will, at one time or another we have all pretty much experienced this, and after being on board for a while it just stopped happening. I don't know if it's a learning curve for the system or what?
I went back and reset my settings a few times, I marked them for no notifications then reloaded the page and selected them again. They started working.
I now use the rss feed with Google reader and get 100% notification by author and in the order they were written.
After that I hope you get a better answer, dusty