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My updates list has been funky, too.
One other report so far of the backup being deleted during the upgrade. This, I think, could be a potentially serious problem. Also, having to redo an entire backup afterward could be a bandwidth issue as well. Not to mention it has got to be adding to the congestion on Apple's servers. That's their issue, but would still make things slow for the end users.
I submitted a bug report to Apple about the backup. I'm a real stickler for backups and I do not like having had mine deleted like that.
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