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About your problem:
By default, JDownloader offers you the best video,audio,image,subtitle
But there is a new Column called "Variant" to choose the variant you want:
If this column is no visible, you can restore it:
If you prefer the old JDownloader 09 style, or want to choose what which variants should be preferred, you have to open the plugin settings:
This setup, for example, would add all available qualities to the linkgrabber.
If this is not enough for you, or if you want to know why we do not use the old style any more, open the advanced option, and enable extended variants.
After a JDownloader restart, you can now choose from ~160 variants.
A single video thus could result in 160 Linkgrabber entries (even more if there are subtitles)
You wouldn't want that