Recording to a Tascam DR40 from the cue outputs, sound is recorded fine from cued tracks & inputs, but transitions from scenes are not recorded.
Do I have to cue scenes?
I could record from main outs and monitor from headphones I guess…
No. Cued tracks are not affected by the master track, though. Could that have caused problems with your recordings?
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I guess you mean scenes concerning XLEVEL. This affect MAIN Output only. You can’t use scenes for CUE LEVEL, but you can modulate XVOL instead (AMP page).
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One suggestion : record from headphones out 
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Thanks! Hadn’t realised I needed to set separate cue levels. Was wondering why the levels were different to main!
Yes that could be. My scene locked parameters were on track 8 master