As expected, turning off Antispam, Cache and so on just was a waste of time, it didn’t change anything. (How should it, after all, as they’re all completely unrelated to media upload.)
What did you change in the media uploader from 3.9.0 to 3.9.1 that made things break?
As I said, I had exactly the same plugins with exactly the same theme in 3.9.0, yet the instant media upload worked just fine.