It's been a few months, and I'd partly given up trying to get this working on my server. Mainly because I'd copied all the bluerays I had through my windows laptop.
I recently got some more and it became an issue again ripping things on my laptop.
I ended up deciding it must be to be with caddy, so ordered a cheap usb->13 pin sata adapter from ebay -
http://www.ebay.co.uk/itm/252088099863
I plugged this in and was worried to find that it's also based on an initio chipset - however a usb2 one ....
This works now I believe. I am able to run makemkvcon info disc:0 which outputs lots of info about the disc and no errors. With my old caddy I got tons of errors at this point.
I then tried to run makemkvcon --minlength=4800 mkv all disc:0 /media/raid/output/ which whizzed the drive up and then it exited.
Adding debug didn't tell me much more.
I'm going to try and test tonight if it works using the UI - the machine is a headless server and was doing this from my chromebook which has no xserver.
I'll post here later today, I hope