When one did the rsync was mysqld service still running? or was that 'Nuked'? If server was setup following recommendations, cron job/task could still have been running every minute ... reads and writes to DB. Don't think there is an option/switch for rsync to halt services, do the copy, restart services ... it's just a raw copy.
Also, rsync done with preserve ownerships/permissions as everything in /var/mysql/ is tagged belonging to the mysql user. Howard has already said if those files are located properly and I'll add ownerships/permissions, then possibly things ok.
Rsync method is a last hope effort me thinks (yes, I've had to do two of those - one did ok ... cause I made sure mysql service not running before rsync ... the other had issues with some tables - which, thankfully, were not critical to getting the new site up and running.
'spirit of sharing', Ken