I’m also having the same problem. Plugin Updates work fine, but WordPress 3.7 (or the new 3.7.1 update) fail. Manual updating via copying over the wordpress core files worked to update to 3.7, but the 3.7.1 update fails again.
I then changed nginx.conf and added in the http part (read it somewhere else – it’s a solution to get the update through, but no solution on to why it’s soooo slow):
fastcgi_read_timeout 600s;
this worked. However Updates still take forever. Sometimes also when me or someone else wants to write a comment, it takes up to 5 seconds to register the comment. Everything else for me is blazing fast (the server is completly overpowered, just serving some big files (about 5TB month) and two websites with about 300.000 visitors/month (i7, 8GB RAM, 200Mbit up/down).
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