After a bit more playing I have found that removing backupmenu doesn't fix the problem, and reinstalling stock kernel doesn't fix it either. Even with no boot menu at all and no special kernel I can still get the boot loop.

Pressing the power button at the right time might have nothing to do with it either If I leave it long it enough it will eventually get there, usually after 3 or 4 reboots.

I do want to backup and then reflash still just to confirm it is not the hardware dying, but I haven't had time yet and I don't reboot very often anyway. I can't see anything else I have installed which could cause boot problems though.