Thank you for reporting this behavior.
We will research what is causing it and fix it if it appears related to RadEditor.
Currently, you can render the content area of RadEditor for SharePoint 2010 as an editable iframe and set the CssFiles property to point to your own css file. Therefore only the classes defined in the css file will be loaded in the Apply Class dropdown:
ConfigFile xml file:
imports a CSS file in the head of the editable iframe content area of RadEditor. This means that this property works only when the content area is rendered as an iframe. If we import a css file when the div mode is enabled this will ruin the design of the entire page, because the div content area is part of the page. The iframe is another document.
the Telerik team
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