OK - I'm done with El Capitan - Not going to bother anymore.
I wiped the SSD, did an internet install with a pristine version of Lion. Installed the release version of El Captian (10.11.1). Tested the reboot - worked fine.
Did a migration of all my data and apps - will NOT REBOOT.
The only other thing I can think of is to manually bring everything across one at a time and see if I can find what causes it.
But seriously - I work - I have 3 kids under 9 and I look after my mother who has dementia. I cannot do Apple's work for them.
I was on the Windows Insider program - and had early builds of Windows 10 that were better behaved than this.
Sorry Apple - you've lost me now - I'm not bothering to upgrade my 2012 Macbook Pro retina now - it can stay with Yosemite until next year's iteration - and if that doesn't work - then it can stay with Yosemite until it's end of life.