Yep, it was a cross between Github update and the process I had to perform on one of my sites, so sorry for the confusion. I'm still catching up with all the changes
One site I had simply refused to work and I had to install the various zips one by one to get up and running. I haven't found the cause yet but I have a backup of that site before I upgraded, so I intend to look at it.
This process should work, despite being tedious. I would try an avoid FTP as the permissions can get messed up depending on how your web host has applied them.
JUST to clarify though. Are these latest issues on a new build? i.e a new Joomla & Fabrik installation?