Unfortunately, this is a known issue (see below the previous posts) with the Internet Explorer ActiveX control (used by the portals) when used in a particular context. The work around as suggested in the thread below to change the authentication scheme of the web site.
Portal Manager dont like popups:
Cookies lost when opening new windows from portals:
FYI, I can access the Gmail in portal (http://mail.google.com/mail).
Hope this helps.