I have a similar issue that the changes in design view is not persisted into the source view.

It's easy to repeat in VS2008 SP1 (I'm using Vista Enterprise):

1. Switch to Split View to see the problem easily
2. Create a Panel control
3. Drag a RadioButtonList control to the Panel control
4. Select Edit Items from the smart tag menu of the RadioButtonList control
5. Add 4-5 items (just Add, do not specify any Text or Value)
6. Click OK.  The design view display is correct, and the change MIGHT be persisted to source code
7. Select Edit Items again, and delete 2-3 items, then OK
8. Repeat the Add/Delete items a few times, you should see that the changes won't be persisted to source code (design view is correct)
   

The following issue in Connect looks similar:

https://connect.microsoft.com/VisualStudio/feedback/ViewFeedback.aspx?FeedbackID=390933

Unfortunately the official reply was that there will be no fix in the current version.  It is completely unacceptable if that is true.  I agree with one of the feedback in the above Connect thread that this will make VS2008 virtually useless (or at least the design view useless) because we might risk losing all our work unknowingly as the design view is correct, but not saved to source code.

I sincerely hope that MS will take this issue seriously.

Regards