Update: This has now been fixed. Please see my new post.
The ASP.NET designer in Visual Studio 2008 has a bug where the aspx code might not get updated when making changes in the design view- this only happens under certain conditions. Currently (14th March 2009), there is no fix for this known issue. When a fix is made available it will be posted to the Visual Web Developer Team Blog.
In the meantime as a workaround, I am performing any designer required work on a new page in the project, and copying the generated aspx code manually.