Hi Ross,
If I understand correctly, this situation always occurs for you within content pages, and isn't resolved by opening/closing the editor, or by deleting the ReflectedSchemas directory.
First, let's have you close down any instances of VWD, and again delete the ReflectedSchemas directory. Next, crank up VWD and open only the file that experiences the issue. Verify the issue still occurs, and close VWD. Next, crack open the schemas.xml file within the ReflectedSchemas directory. This is the file that we use to cache all the reflection that we've done to create the schemas that the markup intellisense engine uses for intellisense. In the scenario you've just executed, we should have created two schemas (more if you reference user/custom controls within the opened page). One is for standard web forms, and the other is for content pages. Search for "__DESIGNER_ASP_CONTENT" within this file, then open the file referenced to by the SchemaPath attribute on the same line.
This should be the file that we use for intellisense within content pages. If you open this file, you should notice one top-level element with type="System.Web.UI.WebControls.ContentDef". If you look at the definition of the type, you should see that it contains an <xsd:group ref="System.Web.UI.ControlExtendedElementsGroupDef" />. This group's definition should contain a whole bunch of valid top-level asp controls.
Can you let us know how this checks out? If everything looks good at this point, I think I would need to see your content page to investigate further. Thanks for your input, we really do appreciate it.
-- Todd