It appears that Visual Studio is unable to pick the correct namespace based on the registered controls.
I have resolved this issue by moving the charting registration to the top of the list. This result in the designer files being generated correctly again. The namespace for asp:Chart controls is correct too.
So my controls section in the web.config has gone from this:
<pages>
<controls>
<add tagPrefix="asp" namespace="System.Web.UI" assembly="System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<add tagPrefix="asp" namespace="System.Web.UI.WebControls" assembly="System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<add tagPrefix="asp" namespace="System.Web.UI.DataVisualization.Charting" assembly="System.Web.DataVisualization, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35"/>
</controls>
</pages>
to this:
<pages>
<controls>
<add tagPrefix="asp" namespace="System.Web.UI.DataVisualization.Charting" assembly="System.Web.DataVisualization, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35"/>
<add tagPrefix="asp" namespace="System.Web.UI" assembly="System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<add tagPrefix="asp" namespace="System.Web.UI.WebControls" assembly="System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
</controls>
</pages>
I still think there's a bug in VS that caused this behaviour.