The following are suggestions you can use to help isolate problems related to EMI:
1. Check the frequency spectrum of an EMI test. If there is unusual high frequency peaks such as discrete and periodic step response curve, it may be caused by clock resonance. You should also check if there is proper termination for clock signals to insure there are no glitchs and overshoot.
2. Check the frequency spectrum to see if there is a 30-100MHz bandwidth wave crest. It may be caused by the power supply. You should check the decoupling of the power rails to ensure they are at the correct target impedance.
3. Check the isolation between power supplies.
4. Plug-in and remove any connectors or cables to isolate noisy sources.