Eric seems to have nailed it with his reply, "I think if you click on the icon they goes in the upper section and refresh, and if you click on the counter, they goes in the lower frame but do not refresh the upper section." I was finding the same annoyance and, if I click on the icon, it does refresh the upper section wherease the number goes into the lower frame and you lose the list of messages if you click to read one.

So....try the refresh icon and you should be happy :)