Strange issue with MySql 5.6 replication
Activate the general log on both servers at runtime (beware of doing it when you have a lot of load, as that will make all your queries slower):

SET GLOBAL general_log = 1;


You will find it on datadir/hostname.log, or you can change its location with the general_log_file parameter.

There, all connections and queries sent to the server will be logged. Compare what NaviCat and Workbench are doing to identify a possible problem. You can also check the contents of the binary logs with the utility mysqlbinlog and the changes applied with the commands SHOW MASTER STATUS and SHOW SLAVE STATUS\G on each server, making sure that the replication is not broken (very common in master-master replications).

Remember to disable the general log after you are done:

SET GLOBAL general_log = 0;