This may not be correct or may not work..
In my limited experience such high frequencies are a result of the output diode reverse biased capacitance ringing with transformer secondary leakage inductance. What happens is that when your primary side switch turns on the output diode is reverse biased but before that can happen it has to undergo reverse recovery. During that time it behaves as a short circuit and returns current back into the secondary winding of the transformer. At this stage the primary winding is effectively connected to low impedance, it is connected across the input bus, so that reverse current from the diode is acting on the secondary side leakage inductance.
When the diode finally turns off then, assuming a positive output rail, the cathode races off to some negative voltage and the energy previously placed in the leakage inductance resonates with the reverse biased capacitance of the diode. It's not necessarily something that can be solved easily by use of soft recovery diodes or modifying switching rates. Ultimately you will probably have to attempt to snub the ringing with a series RC network.
Of course it would be worth checking with your scope if the suggested node, output diode cathode, is the source of the problem.
Measure the reverse voltage across the diode. Check in the data sheet to see what its junction capacitance is for that particular level of reverse bias. That will give you a quick guess as to C in the RC network. Use a value 3 times what the data sheet gives at that reverse voltage. Since you already 'know' the ringing frequency you can calculate the required resistance as the impedance of the diode's capacitance as already determined at that frequency. The resistor will dissipate power of Fsupply.CsnubV^2, V will be the negative excursion plus the output voltage. The 1/2 is not there because it will happen at twice the switching frequency. Fortunately with such a low voltage supply that might not be too much.
You will need low inductance components for Rsnub and Csnub and have to mount them very tightly across the diode in order for the snubber to be effective at the frequencies you are seeing.
Genome