After power on with no controller attached, the two USB LEDs flash alternately once per second. When a controller is attached to one of the USB host ports and properly recognized as USB MIDI compliant, the associated LED stops blinking and stays on. Afterwards any messages are transmitted and shown by flashing the MIDI LED.
Is your USB LED turning over from blinking to lighting after plugging in your controller? If not, the controller is not recognized. Did you check another controller?
The ferrites shouldn't be that crucial though I didn't test it without. I guess you bridged the pads?
An image of your board would be helpful.