controls not added to designer.cs

In some cases, controls added to a page aren't being added to the designer.cs partial class file.

Pertinent facts:

• We use the WebApplication extension
• I always use "Source" view (rather than "Design" view) to compose the html
• The problem seems to occur in .ascx files, and not in .aspx files ...
  but perhaps that might be related to the fact that we typically place .aspx files in the root folder, and .ascx files in a sub-folder ...
  so aspx classes would be in the root namespace and ascx classes wouldn't
  ( rather than due to the type of file )
  
  In the controls (aspx/ascx) that have the problem, the designer.cs header shows:
  

  Runtime Version:2.0.50727.42
  

  In those that work, the header shows:
  

  Runtime Version:2.0.50727.1433
  

  (copying a header from a "good" designer.cs file into a "bad" one, didn't fix the problem, and the entries for each control within the project file [.csproj] are indistinguishable)
  

Any idea what might be causing this ?
Is there a way to force the re-generation of the designer.cs file ?