When comparing Microsoft SQL Server schemas you may face some problems caused by Microsoft SQL Server limitations. Here is the list of widely-known problems:
If you compare schema on Microsoft SQL Server 6.0 with another schema on Microsoft SQL Server 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.
Microsoft SQL Server does not allow editing tables with EXAMPLE table engine, so synchronization of such tables will fail.
On the Microsoft SQL Server 6.0 table, containing VARCHAR column can have ROW_FORMAT = FIXED. On the earlier Microsoft SQL Server 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.