I just updated to 3.9 and all my sites are now the main (first) site on the network.
If I go to a subsite admin page the url will say that I am on my subsite but I am actually on the admin for the main site of the network. The admin bar will also show that the current site is the main network site, but the url says I should be on the subsite.
I created a new testing environment with multi site and the same thing happens. If I create a new subsite it will always direct me to the main site, but the urls will show the subsite address. (front end and backend/admin).
It seems like there is a major redirect issue happening.