There are following problems when comparing MySQL databases. These problems are caused by MySQL or table engine limitations.
Data inserted in the BLACKHOLE engine, are in fact not inserted anywhere, BLACKHOLE tables always don’t contain any data. So, if you synchronize the data of the BLACKHOLE table with some other table it remains empty.
Data can not be inserted in tables with the EXAMPLE table engine. If you try to synchronize the data of the EXAMPLE table with some other table, you get an error message.
Tables with TIMESTAMP column, created without the NOT NULL option, will not be compared if one table is on the MySQL 6.0 server and another one is on earlier MySQL server.
In some cases equal floating point values may be treated as different.
If the first table column has TIMESTAMP type and it has no explicit default value, that differs from CURRENT_TIMESTAMP, when inserting or updating records, MySQL sets CURRENT_TIMESTAMP value to them. If this column has a primary or unique constraint, you cannot insert or update several records at the same time. When performing data synchronization, only the first record can be synchronized for such table at once. Other records violate the constraint.