I'm using a templated user controls on some of my pages (similar to http://msdn.microsoft.com/library/default.asp?url=/library/en-us/cpguide/html/cpconcreatingtemplatedusercontrol.asp ).  Rather than register the control each time I need it, I have the control registered in the Web.config file for the site.  When converting a page with the user control to Web Application format, I get the following warning:

Generation of designer file failed: Type 'System.Web.UI.UserControl' does not have a public property named 'MessageTemplate'

If I register the user control on the page (with the prefix changed to prevent duplicate registration), it compiles with no complaint.  Changing it back again brings the warning back.

Is there a solution so I don't have to register the user control each time and don't get the warnings?

It seems that the following thread details the root of the problem and the lack of a solution at this time:
http://forums.asp.net/thread/1281809.aspx

Here's to hoping that the eventual fix to the problem also fixes the "errors" that appear when a default master page is set in the web.config file.