Hello,
That behavior makes me think on signal integrity issues, as you mentioned before on your measures.
Since it is a custom board design and manufacturing technology are different from NXP reference board, and board related parameters may differ from initial DDR script, so please try tunning:
ODTImpedance
Desired ODT impedance in Ohm. Valid values for DDR4=240,120,80,60,40. Valid values for DDR3L=high-impedance,120,60,40. Valid values for LPDDR4=240,120,80,60,40
TxImpedance
Write Driver Impedance for DQ/DQS in ohm (Valid values for all DDR type= 240, 120, 80, 60, 48, 40, 34)
ATxImpedance
Write Driver Impedance for Address/Command (AC) bus in ohm (Valid values for all DDR type = 120, 60, 40, 30, 24, 20)
Did you check signal integrity with a lower clock speed?
Best regards.