We discovered an issue with SC5000 1.3.1 build when used with Serato. It seems that after performing the update 1.3.1 update, the deck will only control deck 1 within Serato DJ. We have since pulled the 1.3.1 download links and are investigating this with the highest priority. If you are suffering this issue please comment and follow this thread for the latest update and fix.
We deeply apologize for this inconvenience and will have more information very soon.