What kind of member validation do you have currently? Email, admin/user?
No not currently. If you've got ftp access to your ipb files, I might be a temporary work around you can try. But for included support, there would need to be some changes to do this.
I can't think of anything obvious that would cause this. I would need full board access to troubleshoot this further. Assuming this is happening across various IPB functions though, I would probably recommend trying with them first because I've never encountered this before and they would have a better idea where to first start.
Are you using the time delay feature? If so, it should be possible to flag selected members as "not welcomed" and they would be retroactively picked up by the welcome task.