Not knowing how you've mapped the controls, it's hard to say, and unfortunately we don't provide much support for 3rd party hardware.
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I'm using a Traktor Kontrol F1 with Rekordbox 5 and, while playing 2 songs in sync mode, if I select a deck to be applied with an effect, it leads to the songs being slightly unsynchronized but enough to have a bad sound. If I deselect the deck the sync comes back.
This behaviour doesn't apear without the controller.
Also, it's impossible to select multiple decks to be applied with the same effect. If I select Deck 1 and I select deck 2, it deselects deck 1. And it deselects deck 2 if I click on Deck 1.
This behaviour is not the same without the controller.
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Not knowing how you've mapped the controls, it's hard to say, and unfortunately we don't provide much support for 3rd party hardware.