Harmony Elite conflict with System Automation

Take a digital (S/Pdif) feed from the television to the NDX, get the Harmony to select that input into the NDX and then it'll all work fine.

Thanks for your help Huge, sounds like an easy fix. Wish I'd studied electronics!  I didn't mention the sound is actually coming from a bluray hd recorder via scart/cinch adapter. It's a Panasonic DMR-BCT720 and it has a TosLink digital out, so what exactly do I need in terms of adapter/cable to get the TosLink talking to the S/Pdif?

TosLink is S/Pdif!

You need a TosLink to TosLink optical fibre (aka an optical 'cable').  One end goes into the source (try it into the TV rather than the BlueRay as you may get TV sound through the HiFi as well (much clearer the the inbuilt speakers), the other end goes into the NDX.  Select the NDX's optical in and there you go.  If you don't get sound make sure the Blueray and TV are set to output 2 chanel stereo (to the HDMI for the BlueRay and to the optical out for the TV).

If it still doesn't work, take the optical feed direct from the BlueRay.

I have optical from TV to NDX & thats the 'Digital-3' input on the app.  Its very easy to set up.     Connecting to TV means you get the sound you see on TV - freeview, BlueRay, Sky  -    Select 2 channel & PCM if you have it in TV options.     The NDX-Nait System Automation needs to select NDX & Digi-3 to play.

"TosLink is S/Pdif!" Doh! :-)

Ok, well since I've already got an Apple TV going into the S/Pdif on the NDX, I suppose there's a Y-splitter thingy I can use at the TV/Apple TV end?

Never mind my last post, I got it now and it works great via the TV and Digital 3. My setup dates back to the day when my old Apple TV wouldn't send the sound over hdmi. Thanks again Mike-B and Huge for your help.