Users were being logged out any time they left the Home page to any other page on the site. I traced the problem back to Flashboard and a line in ViewFlashBoard.ascx.
By adding the PortalID to the query string, the issue was resolved.
<iframe id="flashboard" src="<%=me.ResolveClientUrl("flashboard.aspx")%>?moduleid=<%=Me.ModuleId%>&portalid=<%=Me.PortalId%>" width="<%=Width%>px" height="<%=Height%>px" hspace="0" marginheight="0" marginwidth="0" vspace="0" scrolling="no" frameborder="no"></iframe>
I don't see the problem happening on your site, but I can reproduce it consistently on mine. I may be related to child portals which I am using, but I haven't test that yet.
Thanks,
Rob