I tested several links, and works fine (flashgot and JDownloader 2). And I don't understand why you are using an external tool to download videos, if JDownloader is the best doing it.
Go to the tab Settings--->Plugins---->Look for the plugin of youtube and you can setting the plugin there.
P.D.: Remember that Flashgot is an external tool, and if you have problem with it, you need to ask to the support in the flashgot website.
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