I deleted an activation key, but I still can't signup with that username? Delete the user from Network->Users and delete the activation key.
Is it safe to delete keys from otherwise active users? Yes, as far as I know. I don't know why the activation key for activated users remains behind. But they appear to delete automagicaly after "a while" anyway.
Some users have an activation key in $wpdb->users? That is normal. This plugin doesn't touch those keys, only the ones in $wpdb->signup.
Requires: 3.5 or higher Compatible up to: 3.7.1 Last Updated: 2013-11-11 Downloads: 10,059