My issue was I had a lot of spammers registrations that signed up in dec 2012. They didn't activate their accounts until recently via the email confirmation. So have a look at your 'Users Awaiting Confirmation' group and if necessary clean/dump it. This is what happened to me and I was so confused as I'd turn off registations yet they were still registering, but they wern't actually registering at that point, they were simply activating accounts that they registered in the past. Take a look at the signup date of some of the new accounts as look at the registration date.
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BTW thanks to everyone who chipped in on this post to help really cool. One question tho, I want to either mass move all the 90000 spammers from 'Users Awaiting Email Confirmation' to either 'Banned by Moderators' group or just delete them. THe problem is in the prune users option in the backend it only seems to do it in around 1000 at a time. Then I have to do it again. This is really time consuming is there a better way ? I've heard running direct database commands is risky.