I have noticed that when changing the notifications on the forums page, the changes are not saved (I am using Firefox, MS Asp.Net and the trunk version). The CheckedChanged event is not called. I fixed this by setting EnableViewState to false in the repeater:
<asp:Repeater id="rptForums" runat="server" EnableViewState="False">
Maybe this is of any help. PS.: I like MojoPortal, it is very clean, simple and easy to understand.