Guys - I has just written a HUGE answer with all information. Seriously spent 30 minutes putting stuff on pastebin etc.

But as I was re-reading my ipega media gamepad controller.cfg file before I pressed the submit I noticed the

input_enable_hotkey_btn = "157"

Now. I SWEAR to you last time I read that file it was correctly mapped to the SELECT button on the Ipega (10)

BUT I have messed in the retroarch.cfg file since then to change the driver from udev to sdl2 (only way to get that controller to work with more than just the d-pad in games). I have probably NOT checked it since.

I went in to the ipega file, changed the 157 to 10. Did not even reboot the retropie, just started the controller. Closed my eyes in Centipede, and pressed Select and Start.

AND

Found myself back at the Retropie main menu. What the?

Spent all day looking for something, when a simple double check would have netted the correct result in 2 minutes. I don't know how that file changed. I'm sure it's something myself or the kids have done while messing about. I don't remember doing it so I'll blame the kids because I can.

It's all working now.

Of course, now my son wants to connect an XBOX controller as a second Joypad. More reading to do.

Thanks so much guys. Sorry to screw up but without you guys asking me to paste my config files I would not have noticed the changes that broke it.