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Sorry for the lengthy title, I'll elaborate. I love the fact that I can be on Stackoverflow and get notifications about a question on programmer.stackexchange, and vice versa, but I've realized that this doesn't happen the next day.

For example, if I ask a question on superuser and lounge at Stackoverflow, I'll get the alert when someone replies. If, however, I ask a question, turn my computer off and go to sleep, and then open Stackoverflow the next day, I don't get the notification until I go to superuser.

Is this intentional or a bug?

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Are you referring to the banner at the top of the page? If so that's per-site. However, you also get a notice in your inbox that works on any site in the network. –  Nick Craver Mar 23 '12 at 1:18
@NickCraver, Yeah, I'm talking about those neat little red numbers by the inbox. Which DOESN'T work on any site after logging back on the next day. –  mowwwalker Mar 23 '12 at 1:19
Are you refreshing the page at all, or just resuming your computer from standby or similar? The inbox pulls from the same place regardless of which site you're on... –  Nick Craver Mar 23 '12 at 1:40
@NickCraver, I turn the computer, open up Chrome, and browse Stackoverflow and the top questions on Stackexchange for a while. I often won't realize I have a notification until, by chance, I end up visiting the site the notification is from. –  mowwwalker Mar 23 '12 at 1:46
Do you have user scripts running? There's really no reason you should see the inbox on one site and not another, unless you just weren't logged in on whatever site you were browsing. –  Nick Craver Mar 23 '12 at 1:48
@NickCraver, Nope, it keeps me logged on. I'll check the log for javascript errors next time. Let me know if you want to test anything. In the way of user scripts, though, I am using adblock. –  mowwwalker Mar 23 '12 at 1:53

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