>When I go to Add New Item / Web Form, I no longer see the following two check boxes:
>
>(1) Place code in separate file
>(2) Select master page
>
>I do not know where they went, but these options have disappeared.

Have you somehow 'downgraded' to .NET framework 1.0 ?

BTW, I think the code is in the separate file by default (I never even noticed this option).