I suppose FileFilters is not working for the first time only, that is a known bug of RadAsyncUpload control and also file filtering is available with Silverlight and Flash module only. Please have a look into this forum thread which discuss the same scenario.
RadAsyncUpload control uses Silverlight and Flash upload modules based on that plugins. The file filtering is available only with them only under IE9- browsers. Under the rest of the browsers the filtering is not support. Keep in mind that the extension validation is working everywhere.
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