1) please execute
SHOW GLOBAL VARIABLES LIKE '%innodb_lock_wait_timeout%';
. and paste the result here.
It looks very much like some other application used and locked the tables (for backup for instance) while sync was running. If a transaction on an InnoDB table cannot be committed in innodb_lock_wait_timeout-time it is rolled back. Do you get the same error for the same tables if you try again?
'innodb_lock_wait_timeout' variable cannot be set dynamically – it must be set at startup (typically in configuration file).
2) Also, please give us the sample data for both source and target databases along with their structure.
3) Please tell exact MySQL server version?
FYI : http://forums.mysql.com/read.php?22,206434,246034#msg-246034