Hello braxus,
If you have all boxes off, you should be able to automatically be upgraded. So it is a bug but I am pretty sure I have fixed this issue for my current branch.
For the moment what you can do is to go into the debug mode, go to the new era screen, then you will be able to change manually the new era of your civilization.
I am working currently on another project, that's why I am not very active but I will come back soon to mod on DoaNE.
Sorry for that.