Use user control in the same folder as the page

If you register it in the page or user control instead of the web.config it will load properly. Add the following to the top of the page.

<%@ Register TagPrefix="MyControlTagPrefix" TagName="MyControlTagName" Src="~/MyFolder/MyControl.ascx" %>

This limitation is by design due to an internal design consideration re: performance.

See here for further info.

Remarks

The TagPrefixInfo class allows you to programmatically access and modify tag-prefix information stored in a configuration file. It provides the same functionality as the ASP.NET @Register directive. Tag prefixes associate a "namespace" in ASP.NET to the assemblies and namespaces that must be included for custom controls and user controls to work properly. TagPrefixInfo objects are stored as members of a TagPrefixCollection object. The TagPrefixCollection class allows you to programmatically access and modify the controls subsection of the pages section of a configuration file.

TagPrefixInfo objects are added to the collection using the add element and specifying a value for the tagPrefix attribute along with values for other relevant attributes. The other required information varies based on the kind of control you will use with the specified tag prefix:

• If it is a user control, you must define the TagPrefix, TagName, and Source properties.
• If it is a custom control, you must define the TagPrefix, Namespace, and Assembly properties. The Assembly property is not required if the control is in the application code directory. The same tagPrefix value can be used to map to multiple assemblies or namespaces.

Note When a source is specified, the user control itself must not be in the same directory as the page. If it is, you get a run-time error when you attempt to load the page.