You can add the http yourself:
<%="http://" & PortalSettings.PortalAlias.HTTPAlias%>
This should take you to the correct page even if you set a home page.

 The logo skin object uses this code (in DNN5 VB):

Private Sub Page_Load(ByVal sender As System.Object, ByVal e As System.EventArgs) Handles MyBase.Load
            Try

                ' public attributes
                If BorderWidth <> "" Then
                    imgLogo.BorderWidth = System.Web.UI.WebControls.Unit.Parse(BorderWidth)
                End If

                If PortalSettings.LogoFile <> "" Then
                    imgLogo.ImageUrl = PortalSettings.HomeDirectory & PortalSettings.LogoFile
                Else
                    imgLogo.Visible = False
                End If
                imgLogo.AlternateText = PortalSettings.PortalName

                hypLogo.ToolTip = PortalSettings.PortalName

                If PortalSettings.HomeTabId <> -1 Then
                    ' use portal home page specified
                    hypLogo.NavigateUrl = NavigateURL(PortalSettings.HomeTabId)
                Else
                    ' use site root
                    If Host.UseFriendlyUrls Then
                        hypLogo.NavigateUrl = FriendlyUrl(Nothing, "~/", PortalSettings)
                    Else
                        hypLogo.NavigateUrl = "~/"
                    End If
                End If

            Catch exc As Exception    'Module failed to load
                ProcessModuleLoadException(Me, exc)
            End Try
        End Sub

 There's no direct way to read this AFAIK.