I cannot reproduce the issue you are describing. Implementing a custom column that inherits from Telerik.Web.UI.GridTemplateColumn
seems to work OK with the RadGrid designer, provided that you properly reference both the Telerik.Web.UI assembly and your custom column in the .aspx page.
If the problem persists, consider opening a regular support ticket where you can send us some test project we can debug locally. This will help use better identify the cause for this issue and assist you further.
All the best,
the Telerik team
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