So, I had my appointment with the Apple store Genius.
They pulled their LED display from out back, plugged it into my MacBook Retina, and I set about demonstrating the issue.
My appointment was only 20 minutes, and I could not demonstrate it, however they let me continue whilst they served other customers.
After an hour, I was about to give up, when I noticed he had plugged the screen into a different port on the computer to the one I usually do.
We switched the cable over to the other port and rebooted.
10 minutes later the issue happened, much to my relief that I was able to demonstrate it.
Now, he told me that he had a similar issue a couple of days back, and it turned out to be the monitor cable, however we noticed that the second port was worn (the connector was not held in as well.)
The machine is only a few months old, so they replaced the whole motherboard (Logic board.)
I went home, the connector now fits in firmly, and I started using my machine normally ... it froze up again within an hour - I had just clicked 'send' on an email.
It seemed likely that maybe the monitor was at fault, so today I purchased a brand new 27" Thunderbolt display.
Guess what .... new logic board, new monitor, and it still happens.
(I might keep the monitor though - it's pretty amazing)
Apple had reset absolutely everything in store.
Going to try a competitors virtualisation software and see if I get the same issues - hoping this might give me a comparison.