OK so I set up kodi, pi and x-newa. They work and play the files without the blink. Its a bit too easy to drop back out of X-NEWA to kodi though and the Samsung Smarthub remote doesn't blend as seamlessly with x-newa as it does with Fred's app.
Samsung have said that they think the blink is caused by the TV trying to upscale the 50fps stream to UHD. Not sure why it would do that with an interlaced stream. Apparently that's why the lower spec telly's cope as they don't have the upscale functionality.
Would still like a good tool to look at resolution, interlace and frame rate of the recorded files. It would be nice to get to a definitive 'It happens with this type of recording' statement.
Server: Ci5 2500k, 3GB, Windows Server 2012, nPVR 3.5.7. 2xWinTV-DVB-T USB, 1xWinTV-DVB-T PCI, 2 x BlackGold DVB-T, 1xPCTV290E and 1xPCTV460E on Astra 28.2 E.
clients: RPI2, Acer R3700, PCH-A110, NUC, 3xSamsung Smart TV