The problem was with a site that had such a big field in wp_[site_id]_options that the entire table was truncated, probably due to a mysql timeout. We move sites around via mysql export and import and this one had been malfunctioning for a while. Dropped that site and network upgrade ran to completion.
That said, the typical problems can be solved by verifying site connectivity and looking at subcomponents (dns works. siteurl, home and domain all in congruence. no redirects on web server affecting site).
regards,
Scott
