The notifications that are at the bottom of the site, for each section on the site... have never worked. Suggestions for repair?

Define, what you mean by "never worked".

Did you register, and never received any messages?

Is you system sending emails OK?

The question: is it Notification issue, or your email issue.

Yesterday I tested after turning the notifications blocks back on. I hid them after they weren't working... back maybe after our upgrade to 2.0, its been so long I forget now. Anyway staff were complaining that they had notifications set and never got any emails so I just hid the blocks and forgot about it.

I created items yesterday and my other admin did get an email but I didn't. So it doesn't send me a notice if I created the item, that makes sense. I will get the other admin to create some new items and test it. Yesterday I went through all of my modules and ran the update feature... hoping that if something was not right after our server move that it might be resolved with this. It did seem to fix our issue with not being able to upload items on forum posts.

Notifications work via email but not via PM.

Also when a new PM is received, there is no notification either.

Getting closer... the notifications are now coming to my PM box but I never get an email to tell me I have a new PM either.