The chat counter in the $c.do page shows more chats waiting than there actually are, and when an agent accepts the chat, it says that the queue is currently empty
There is at least 1 chat that is in a "waiting" state for the queue experiencing the issue. It does not matter whether the chat is active or not, if the state is waiting, you will see the waiting number for the queue incremented +1 for every chat in a state of 'waiting'.
Delete the problem chat records
Setting the chats to "Active = false" will not resolve the issue as the queue looks for chats in a 'waiting' state regardless of whether they are "active"