When comparing MySQL schemas you may face some problems caused by MySQL limitations. Here is the list of widely-known problems:
If you compare schema on MySQL 6.0 with another schema on MySQL 4 or 5.0, and there are tables with TIMESTAMP column, status of such tables will always be different even if they have the same structure or they were synchronized.
MySQL does not allow editing tables with EXAMPLE table engine, so synchronization of such tables will fail.
On the MySQL 6.0 table, containing VARCHAR column can have ROW_FORMAT = FIXED. On the earlier MySQL version you may execute ALTER TABLE … ROW_FORMAT = FIXED but it does not do anything. So, such tables will have Different comparison status even if after their synchronization.