Always on Wordpress 3, right? Me too. I had a network on 3 that set up so slick...I hadn't anticipated any problems with 4.
I think that is part of the reason I was a little flippant with the setup initially -- "oh, well, I'll just set it up wrong and move it to the right place later" -- and that was what bit me.
I am really stumped as to what is going on with yours now. I know that once I was very particular about how I set it up, it all went together well.
I do know that my server is specifically set up to be good for Wordpress 4. So if there was a server setting, I wouldn't know about that. I have a unique ability to crash servers, so I rely on my hosting company to set mine up.
Seriously. Bought a server once, crashed it within 5 minutes. Had to have an expensive technician come out and format and rebuild the whole thing. It took him ours, muttering, "HOW did you do this???" the entire time. Shrug.
I don't do servers. (grin)