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Whenever I go to read a new PM or reply to an old one, the white number on a red background stays the same. If I then go and check my alerts, the number updates. Can the number also update when I check the inbox?
That's pretty common on other boards including Smogon on vB. It's such a minor issue and would be extremely low priority if anyone were to consider fixing it. If an administrator sees this then it might get done but I wouldn't count on it.