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On your first point: how would you tell XOOPS which database to use? If I were you, I would make an SQL dump of them both, and compare them. Then, cosolidate them into one, and use only one.
About the login problem, it may be that you're running a firewall software that blocks http header information with cookies. Make sure your site is added to the trusted sites list, or that at least http header information can be sent to the cookie on your machine, and sent from your machine to the site.
Herko