Hi,
I'm just assuming, so if I'm not correct, please clarify.
In case you are using our devkits
https://www.nxp.com/design/development-boards/automotive-motor-control-solutions/magniv-and-s12-solu...
https://www.nxp.com/design/development-boards/automotive-motor-control-solutions/magniv-and-s12-solu...
https://www.nxp.com/design/development-boards/automotive-motor-control-solutions/magniv-and-s12-solu...
All three boards are capable of using DC-link shunt resistor to control a 3-ph motor, but the last two can do only this technique (aka "single-shunt" only).
If you are using the MTRCKTSPNZVM128 or MTRCKTSBNZVM128 (physically, it is the same devkit), then I would recommend to verify the jumper settings first according to the Quick start guide and the dedicated application note - there is a different configuration for dual-shunt and for single-shunt.
By the way, in all the cases, the reference voltage is 2.5V and thanks to that, the ADC can see positive and negative currents.
If you see any difference from what you want to achieve and from the description above, please let us know.
Best regards.
Matej