I’ve been messing around with this again today and seem to have got to the bottom of it – removing the Geforce GT 710 and re-enabling the onboard Radeon 4200 seems to have solved the problem. Works perfectly without the need for Vsync, Hard GPU sync or threaded video enabled. I would be interested if anyone knows why.
I was hoping I would get the Geforce working with it so initially I tried replacing the nouveau drivers with the nvidia binary blob – I would not recommend that others try this as from what I gather from https://devtalk.nvidia.com/default/topic/1008518/jetson-tx1/x11-configuration-xrandr-refresh-rates/ the official nvidia drivers only accept predefined modes or modes from a monitor EDID – xrandr won’t change modes with these drivers.
Maybe ATI cards are better suited for CRT displays in Linux as well as Windows?