Whenever you add a reference to framework libarary to the project, open your project file in text editor and remove HintPath attribute from the appropriate Reference tag. This attribute is not necessary for the framework libraries.

You also need to add reference to the NAnt build file for the project by adding line similar to this to <references> section:

<includes name="${nant.settings.currentframework.frameworkassemblydirectory}/System.Web.dll"/>

Of course, replace System.Web.dll with the name of the assembly you are referencing.

Note: There is no need to reference System.dll or mscorelib.dll explicitly. They are always included in the list of references.