We recently identified an issue causing audio to skip or drop out when using the DDJ-1000 with rekordbox dj. The issue occurs when Beat FX are applied to some channels such as Mic and Master. 
We’ve identified the cause of the issue and we’re working on a fix that we aim to make available between late May to mid-June. 
Until the update is ready, you can avoid the issue by setting the software buffer size as low as possible. For details on how to do this, see the ‘Setting utility software’ section in the DDJ-1000 instruction manual.
We’re sorry for any inconvenience this issue causes. Keep checking here and on our social media channels for updates.