10.0.1 migration manager was so buggy I didn't notice this issue before since we had basically given up on it, so I'm not sure if the issue was present in 10.0.1, but in 10.1.1 migration manager fails any migration from an 8.x server where a domain has either web users or unique FTP accounts for subdomains. You get obscure errors about ftpusers, but if you get rid of the web users and set the subdomains back to 'use primary ftp account', it works fine.