>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.

Are you working on a project or a website.

A Website Web form will give you those options.

In a Project, you add a Web content form that will go in a masterpage.

Consistency is seriously lacking.