This is definitely a WP 3.9 issue. On the same server I have 8 other WP sites and the only one with any problems is my main site which I just upgraded to WP 3.9
The other sites have NOT been upgraded and are still working perfectly fine.
My problem is getting worse. I am now getting Error 500 when I try to access WP-ADMIN. I can still go to the main site and it’s up and working with no errors. I just can’t do ANY admin functions now.