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Firstly, please keep your board is good grounded with LSIN. Then please update your measurement details with us, eg. output power, PVDD, Speaker load=?ohm etc.
Based on your report, it is strange to see that 3th harmonic is larger than primary tone @ ~300KHz. It is not reasonable on my side. Please check:
1. please check your power board by changing another power board or adapter to see whether it is caused by different suppression capability of power board at 300KHz and 900KHz;
2. Tuning your EMI filter by adjust inductor and cap to see whether it can be lowered ;
3. Please check our inductor to see whether it is saturation that cause this.