Im not sure why this happens but it happened to me and this is how I solved the problem

Create a department for the different depts that you want and you also need to have one that is linked to all users , i have setup "general enquiries"

generate the code using the html tool for the all users department in my instance "general enquiries"

now when anyone is online "general enquiries" will show as online and the icon changes accordingly, but the users are still presented with the departments to choose the one that they want to talk to regardless.

The code doesnt work when you generate the icon code for "all departments", im no php or techy so I couldnt code a solution but there is clearly a problem with the query that is used for "all departments" within the icon selection as it doesnt look to the child departments for online users.

Hope this helps.