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