You said that when new customers register they don't get "the settings".
But can you see those customers in your Admin area?
When they're on the website, do they show up in the Admin->Tools->Whos-Online area?
Do the old customers show up there too?

It seems to me like you've got two separate databases, and somehow your new customers are seeing a different database for some reason, which as mentioned by someone earlier suggests that a database cluster is out of sync.