I just updated WP to 3.9.1 and Jetpack 3.0.1 (running PowerPress 5.0.7)
My media player was previously set to Flow Player Classic, and when you'd load the page you'd see that player for a brief moment, then it would jump to the MediaElement.js interface.
When I went to the Audio Player settings it showed MediaElement.js as the selected player. If I tried to change it, it would throw me to the Jetpack Omnisearch search box in my WP Admin panel.
I got around this by disabling Omnisearch in Jetpack. I was then able to switch the audio player configuration back and it's working OK.