J721EXCP01EVM

A little bit of looking at schematics shows that the two lights that are out on the Main Processor board are indications of VSYS_IO_3V3 and VSYS_MCUIO_3V3 which are generated from load switches U6 and U22 on the SOM.

U6 generates VDD_IO_3V3_LS from VSYS_3V3 and EN_3V3IO_LDSW; EN_3V3IO_LDSW is the output of GPIO11 for PMIC-B; VDD_IO_3V3_LS directly becomes VSYS_IO_3V3.

U22 generates VDD_MCUIO_3V3_LS from VCCA_3V3 (derived from VSYS_3V3) and EN_MCU3V3_LDSW; EN_MCU3V3_LDSW is the output of GPIO3 for PMIC-A; VDD_MCUIO_3V3_LS directly becomes VSYS_MCUIO_3V3.

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The remaining LED that is lighted is powered by VSYS_3V3.

A couple of ideas: 

TP128 is a spot to measure VCCA_3V3; it is the input voltage to the PMICs; if this was not at the right level, then the board would behave as you are describing. VCCA_3V3 is shut off if VSYS_3V3 is too high. So, in case TP128 shows an incorrect voltage, check VSYS_3V3 at TP1.

Did you write to either PMIC?