Found the last problem, figured it must be something in the TX setup but having not changed anything I was struggling to think how.. After noticing cat pawing at the remote when I woke up I think I know how the change happened as I did leave the TX unattended powered up earlier..
Anyway, PPM First Channel was set to 4 so that is fixed now.
As for original problem, I think the answer to that may well be a visit to specsavers to have my eyes tested, its flashing yellow/blue not yellow green - quite where I got yellow green from I have absolutely no idea at all!
That indicates GPS failsafe enabled, which of course it is because it is the only failsafe which is enabled by default, so its not a problem.. Also, given that it is on by default the thing must have ALWAYS flashed blue/yellow.
I think it can all be summed up as "I am a muppet"
On the plus side it has been raining all day so I would not have been able to go out and fly the thing even if I had figured it out earlier, and in my defence there is no reference to blue/yellow flashing in the manual supplied with it