Chances are something doesn’t line up in the database. The values in wp_options->site_url should the an exact match for the wp_blogs->domain + path values.
I made a post here on the tables needed to change to transfer a multisite. Double-check these values.
For subdomain multisites, your domains should be site1.domain.com and path should be /, where your site_url should be site1.domain.com/.
Also, check your wp_sitemeta->siteurl value, and make sure it makes your blog1’s values.