an authentication cookie from www.somedoamin is not the same as from just somedomain so that part makes sense.
But there is nothing in mojoPortal that is going to change from a www url to a non www url, other than the option to force a specific host name (which you should do for SEO reasons) but then it would always stay the same ie there would not some urls with www and some without, so you must have a link hardcoded somewhere that changes the url or some kind of network issue where something else like a proxy server is changing the urls.
Seems to me that you should force a preferred host name and that should solve the problem.