In Toad for SQL Server, when using the filter on a column in the Database Browser | 'Data' tab, the filter on a particular column only filters the data that is retrieved during the initial fetch, not the rows after the initial fetch.
It is a client side filter in SQL Server, if 999 rows are fetched first and a filter is applied, only the 999 rows are filtered.
Right click the data grid and select "read all rows", then apply the filter again to effect all rows.
To increase the number of rows returned from a query:
1. Select Tools | Options | Database | General.
2. Modify the value for "Number of rows to initially fetch from a query".
Comparing Toad for Oracle and SQL Server:
In Toad for Oracle, a filter on a column does not effect an initial fetch. As Toad for Oracle is able to do the server side filtering because Oracle exposes the servers side cursor while SQL Server does not. The filter works differently for the two databases.