From Sitefinity 3.6 we use embedded templates. If you want to make some changes to the templates you have to map them. So, you could try to map the external template for GenericContentDesigner and see whether you are not able to see your .flv files event with the following explicit setting
Generally this is the default path for .flv files which is used by RadEditor's Flash manager.
If the problem persists you can send us a sample project that illustrates the behavior you are experiencing.
the Telerik team