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There is a preference in the player settings to disable the slip flashing. Chances are the 2nd deck has it set to off. You can also set this in the device preferences.

I have 2 CDK2000 Nexus, DJM900 Nexus and the latest version of Recordbox. The red slip flashing light only lights up on deck 1 and I can't seem to find anywhere to see why this happens.
There is a preference in the player settings to disable the slip flashing. Chances are the 2nd deck has it set to off. You can also set this in the device preferences.

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That's the settings I have in my pane, when the USB stick is inserted a message comes up asking if I want to load the settings but deck 2 doesn't light up.
Go into the settings on deck 2 on the player and see what it shows there.
OK so I am still having issues getting the light working on both decks. All the settings are the same on both decks i.e. slip flashing is on etc. But I still only get it on the left hand deck No.1. I have had several other people look at the setup including one high profile DJ and we still can't work it out.
@Stuart > Are they both running the latest firmware?
Yes everything is up to date
Does it happen if you try just the one deck (non-linked)?
Sorry for the long delay in replying. Ok so here's how it is at the moment.
When linked only a deck number "player 1" will light up red when the crossfader is active on that deck.
Both decks will flash at end of track either linked or single.
You're talking about 3 different things here.
You know slip flashing is different than the end-of-track warning, correct? And you know that "ON AIR" is different as well?
In order for the platter to illuminate red (on-air) you need to have the player number in the display match the audio channel to which it's connected on the mixer, and the mixer itself must be linked along with the players. That way when player number 3, connected to channel 3, has the fader open, the platter will illuminate red instead of white.
My apologies if I had realised it was ON AIR and not Slip Flashing it would of probably helped. Got a strong feeling that the channel / deck number may be the problem. Thanks
If that's what you're referring to, then yes, that's the key. ;)
You can renumber the players in the UTILITY menu, but first you need to disconnect any USB devices, cables and ethernet cables from the player.