Conducted Emission Fail at High Frequency
1) First let's talk about your filter: Check if the resonant frequencies of the capacitors that you are using are high enough. In the resonant frequency your capacitors will behave as resistors. Above the resonant frequency...as inductors.   

IF this is the case, you might test some smaller values of capacitors in parallel with the existing ones (smaller capacitors of a same series usually have higher resonant frequencies).

2) I don't know what switching device you are using (IGBT, MOSFET...), but consider to do some research on RC snubbers in order to attenuate the parasitic currents close to your switching devices.

Best regards