Maybe my system's different, but if I try a manual update without realizing the auto-update's already in progress I get (or got, in earlier versions, haven't tried this recently) a popup warning telling me so.
What kind of pop-up do you get? The only pop-up I get is the green one telling me that the normal update was just completed. What are you getting? We have similar systems. Try testing it with this newer version and see what happens.
It's tricky to set up that kind of test deliberately, since I don't know when auto-update's doing its thing other by catching it "in the act" with Process Explorer or the like, although surfing does tend to get a little sluggish while Setup is hunting for a server. I suppose I could try it when things get sluggish not quite 4 hours from the last green popup. Over the weekend, especially this holiday weekend, probably isn't the best time to try, since we often get only one update on those days.
And that warning popup I mention wasn't a version of the usual bottom-corner notification, it was more or less centered on the screen.
(Edit) Ages ago, on the old Wish-list thread, I'd suggested adding date and time to those notification popups, which would make things a little handier. Especially if you're using that "Show last popup" thing.
