We had the exact same problem. There is no ini setting for that. The only solution is to replace session variable "RegisterUserID" with something like "RegisterUserID_".$user_class_id so it will be different for different siteaccess. To do that you need to hack the user/register.php or make custom module with original register.php changed.
Thank you very much André and Ivo. The session config solution works.
[Session]
SessionNameHandler=custom
SessionNamePerSiteAccess=enabled
SessionNamePrefix=something_
Using a different prefix for each siteaccess of course. (in case anyone else is looking at this)
In addition to these settings, when logged in from one siteaccess, other siteaccess sees the user as logged in as well. (this was one of my concerns, because I have 2 more siteaccess to control the languages)
Tested under Ez Publis 4.3.0, PHP 5.2.8
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