Hi Patricio,
*Can you change the target device (custom board) voltage to 3 V instead of 3.3V and see if it helps. 
* Try to change clock speed for SWD to see if it helps : nrfjprog -c <speed_in_kHz> <other_command>
nrfjprog commands • nRF Command Line Tools • Technical Documentation
* Also since you are using 3rd party module, I strongly recommend to check with them (contact Raytac) to see whether MDBT53V-1M modules ship with APPROTECT and/or ERASEPROTECT enabled, and whether a factory unlock procedure exists.
* Also check ERASEPROTECT status by reading UICR.ERASEPROTECT (0x00FF8020) — if the value is not 0xFFFFFFFF, ERASEPROTECT is active.
Best regards,
Ressa
Hi Patricio,
*Can you change the target device (custom board) voltage to 3 V instead of 3.3V and see if it helps. 
* Try to change clock speed for SWD to see if it helps : nrfjprog -c <speed_in_kHz> <other_command>
nrfjprog commands • nRF Command Line Tools • Technical Documentation
* Also since you are using 3rd party module, I strongly recommend to check with them (contact Raytac) to see whether MDBT53V-1M modules ship with APPROTECT and/or ERASEPROTECT enabled, and whether a factory unlock procedure exists.
* Also check ERASEPROTECT status by reading UICR.ERASEPROTECT (0x00FF8020) — if the value is not 0xFFFFFFFF, ERASEPROTECT is active.
Best regards,
Ressa