@macmanx and WP staff
I don't seem to be having any trouble with my blog now, everything is working fine from what I can work out, though, if I can make a suggestion, there is a news section and it would, perhaps, be a good idea to put on there what is happening before it happens or as it happens. Give people somewhere to go to find out what is going wrong.
An article was finally put up about a week after the changes were made to the "notify me of followup posts", after everyone was running around trying to work out what was wrong.
I think it would have helped a lot too, if you have stated the changes to number of tags/categories as well. Told your users why you had done that and what they need to do now.
It would probably help also if you did one on why you have changed the way topics is now read.
You have a news section, it isn't easy to find, but that should be the first place people go to find out what is happening. I've been doing extra bits on my blog to help explain, but it is what you should be doing. Don't keep users in the dark, it would create less confusion.
Just a suggestion