CDJ Nexus2 2000 - large waveform display not showing, missing hot cues and cannot change to coloured waveform

I have just bought the CDJ Nexus2 2000 to use with 2 other pioneer CDJ 2000's and a DJM 900.

I have added hot cues and loops to a track but when I recall the track after the power has been switched off, then it has only saved the first 3 hot cues and the large waveform will not display, it also won't switch to coloured a waveform.

This only happens once I have 'edited' a track i.e put in various loops and cues. I am using 3 separate USB's for each deck and keep one specific USB to use with the nexus2 2000 so that I can access the extra cue points. 

When I plug my USB into my laptop and check the tracks on the USB via rekord box then the waveform also shows as missing. I then have to delete the track, add it again to the USB to get the coloured large waveform display back but I lose all my cue points.  It seems like once I add more than a few cue points this happens. 

Apologies if I am missing something obvious here but any help would be much appreciated!

All tracks are analysed in Rekord box and then put on USBs.